2001

• Freyhof, J. & Serov, D. V. 2001. Nemacheiline loaches from Central Vietnam with descriptions of a new genus and 14 new species (Cypriniformes: Balitoridae). Ichthyological Exploration of Freshwaters 12(2): 133–191. Reference page. 

2006

• Freyhof, J. , Lieckfeldt, D., Bogutskaya, N. G., Pitra, C. & Ludwig, A., 2006: Phylogenetic position of the Dalmatian genus Phoxinellus and description of the newly proposed genus Delminichthys (Teleostei: Cyprinidae). Molecular Phylogenetics and Evolution, 38 (2): 416–425. DOI: 10.1016/j.ympev.2005.07.024

2008

• Özuluğ, M. & Freyhof, J. 2008. Capoeta turani, a new species of barbel from River Seyhan, Turkey (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters 19(4): 289-296.Reference page. 

2009

• Lang, N.J., Poe, K.J., Renaud, C.B., Gill, H.S., Potter, I.C., Freyhof, J., Naseka, A.M., Cochran, P., Pérex, H.E., Habit, E.M., Kuhajda, B.R., Neely, D.A., Reshetnikov, Y.S., Salnikov, V.B., Stoumboudi, M.Th. & Mayden, R.L. 2009. Novel Relationships among Lampreys (Petromyzontiformes) Revealed by a Taxonomically Comprehensive Molecular Data Set. American Fisheries Society Symposium Reference page. 
• Schöter, C., Özuluğ, M. & Freyhof, J. 2009. Capoeta caelestis, a new species from Göksu River, Turkey (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters 20(3): 229-236.Reference page. 

2012

• Freyhof, J., Erk'akan, F., Özeren, C. & Perdices, A. 2012. An overview of the western Palaearctic loach genus Oxynoemacheilus (Teleosei: Nemacheilidae). Ichthyological Exploration of Freshwaters, 22(4)[2011]: 301–312. Abstract & excerpt Reference page. 
• Levin, B.A., Freyhof, J., Lajbner, Z., Perea, S., Abdoli, A., Gaffaroğlu, M., Özuluğ, M., Rubenyan, H.R., Salnikov, V.B. & Doadrio, I. 2012. Phylogenetic relationships of the algae scraping cyprinid genus Capoeta (Teleostei: Cyprinidae). Molecular Phylogenetics and Evolution 62: 542–549.DOI: 10.1016/j.ympev.2011.09.004Reference page. 
• Yang, L., Arunchalam, M., Sado, T., Levin, B.A., Golubtsov, A. S., Freyhof, J., Friel, J.P., Chen, W.-J., Hirt, M.V., Manickam, R., Agnew, M.K., Simons, A.M., Saitoh, K., Miya, M., Mayden, R.L. & He, S. 2012. Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniforms). Molecular Phylogenetics and Evolution 65: 362–379. DOI: 10.1016/j.ympev.2012.06.007 Reference page. 

2014

• Freyhof, J., Esmaeili, H. R., Sayyadzadeh, G. & Geiger, M., 2014: Review of the crested loaches of the genus Paracobitis from Iran and Iraq with the description of four new species (Teleostei: Nemacheilidae). Ichthyological Exploration of Freshwaters, 25 (1): 11–38. Abstract

2015

• Yang, L., Sado, T., Hirt, M.V., Pasco-Viel, E., Arunachalam, M., Li, J., Wang, X., Freyhof, J., Saitoh, K., Simons, A.M., Miya, M., He, S., & Mayden, R.L. 2015. Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes). Molecular Phylogenetics and Evolution 85: 97–116. DOI: 10.1016/j.ympev.2015.01.014 Reference page. 
• Freyhof, J., Sayyadzadeh, G., Esmaeili, H. R. & Geiger, M., 2015: Review of the genus Paraschistura from Iran with description of six new species (Teleostei: Nemacheilidae). Ichthyological Exploration of Freshwaters, 26 (1): 1–48. Abstract

• Mousavi-Sabet, H.; Vatandoust, S.; Esmaeili, H.R.; Geiger, M.F.; Freyhof, J. 2015. Cobitis avicennae, a new species of spined loach from the Tigris River drainage (Teleostei: Cobitidae). Zootaxa 3914(5): 558–568. DOI: 10.11646/zootaxa.3914.5.4 Reference page. 
• Mousavi-Sabet, H., Sayyadzadeh, G., Esmaeili, H. R., Eagderi, S., Patimar, R. & Freyhof, J., 2015: Paracobitis hircanica, a new crested loach from the southern Caspian Sea basin (Teleostei: Nemacheilidae). Ichthyological Exploration of Freshwaters 25 (4): 339–346. Abstract

• Sayyadzadeh, G., Esmaeili, H. R. & Freyhof, J., 2015: Garra mondica, a new species from the Mond River drainage with remarks on the genus Garra from the Persian Gulf basin in Iran (Teleostei: Cyprinidae). Zootaxa 4048 (1): 75–89. DOI: 10.11646/zootaxa.4048.1.4 Reference page. 

2016

• Freyhof, J. 2016. Redescription of Garra elegans (Günther, 1868), a poorly known species from the Tigris River drainage (Teleostei: Cyprinidae). Zootaxa 4173(5): 496–500. DOI: 10.11646/zootaxa.4173.5.7. Reference page. 
• Freyhof, J. 2016. Oxynoemacheilus karunensis, a new species from the Persian Gulf basin (Teleostei: Nemacheilidae). Zootaxa 4175(1): 94–100. DOI: 10.11646/zootaxa.4175.1.9. Reference page. 
• Freyhof, J., Geiger, M.F., Golzarianpour, K. & Patimar, R. 2016. Sasanidus, a new generic name for Noemacheilus kermanshahensis Bănărescu & Nalbant, with discussion of Ilamnemacheilus and Schistura (Teleostei; Nemacheilidae). Zootaxa 4107(1): 65–80. DOI: 10.11646/zootaxa.4107.1.3. Reference page. 
• Freyhof, J., Abdullah, Y.S., Ararat, K., Ibrahim, H. & Geiger, M.F. 2016. Eidinemacheilus proudlovei, a new subterranean loach from Iraqi Kurdistan (Teleostei; Nemacheilidae). Zootaxa 4173(3): 225–236. DOI: 10.11646/zootaxa.4173.3.2. Reference page. 
• Khaefi, R., Esmaeili, H.R., Sayyadzadeh, G., Geiger, M.F. & Freyhof, J. 2016. Squalius namak, a new chub from Lake Namak basin in Iran (Teleostei: Cyprinidae). Zootaxa 4169(1): 145–159. DOI: 10.11646/zootaxa.4169.1.7. Reference page. 
• Lyon, R.G., Geiger, M.F. & Freyhof, J. 2016. Garra sindhi, a new species from the Jebel Samhan Nature Reserve in Oman (Teleostei: Cyprinidae). Zootaxa 4154(1): 79–88. DOI: 10.11646/zootaxa.4154.1.5. Reference page. 
• Mousavi-Sabet, H., Ganjbakhsh, B., Geiger, M.F. & Freyhof, J. 2016. Redescription of Gobio nigrescens from the Hari River drainage (Teleostei: Cyprinidae). Zootaxa 4114(1): 71–80. DOI: 10.11646/zootaxa.4114.1.4. Reference page. 
• Segherloo, I.H., Ghaedrahmati, N. & Freyhof, J. 2016. Eidinemacheilus, a new generic name for Noemacheilus smithi Greenwood (Teleostei; Nemacheilidae). Zootaxa 4147(4): 466–476. DOI: 10.11646/zootaxa.4147.4.7. Reference page. 
• Zareian, H., Esmaeili, H.R. & Freyhof, J. 2016. Capoeta anamisensis, a new species from the Minab and Hasan Langhi River drainages in Iran (Teleostei: Cyprinidae). Zootaxa 4083(1): 126–142. DOI: 10.11646/zootaxa.4083.1.7.Reference page. 

2017

• Brahimi, A., Freyhof, J., Henrard, A. & Libois, R. 2017. Luciobarbus chelifensis and L. mascarensis, two new species from Algeria (Teleostei: Cyprinidae). Zootaxa 4277(1): 32–50. DOI: 10.11646/zootaxa.4277.1.3. Reference page. 
• Freyhof, J. & Abdullah, Y.S. 2017. Two new species of Oxynoemacheilus from the Tigris drainage in Iraqi Kurdistan (Teleostei: Nemacheilidae). Zootaxa 4238(1): 73–87. DOI: 10.11646/zootaxa.4238.1.5. Reference page. 
• Freyhof, J. & Geiger, M.F. 2017. Oxynoemacheilus zarzianus, a new loach from the Lesser Zab River drainage in Iraqi Kurdistan (Teleostei: Nemacheilidae). Zootaxa 4273(2): 258–270. DOI: 10.11646/zootaxa.4273.2.6. Reference page. 
• Freyhof, J., Kaya, C. & Turan, D. 2017. Oxynoemacheilus kentritensis, a new species from the upper Tigris drainage in Turkey with remarks on O. frenatus (Teleostei: Nemacheilidae). Zootaxa 4258(6): 551–560. DOI: 10.11646/zootaxa.4258.6.4. Reference page. 
• Freyhof, J. & Özuluğ, M. 2017. Oxynoemacheilus hazarensis, a new species from Lake Hazar in Turkey, with remarks on O. euphraticus (Teleostei: Nemacheilidae). Zootaxa 4247(4): 378–390. DOI: 10.11646/zootaxa.4247.4.2. Reference page. 
• Freyhof, J., Özuluğ, M. & Saç, G. 2017. Neotype designation of Aphanius iconii, first reviser action to stabilise the usage of A. fontinalis and A. meridionalis and comments on the family group names of fishes placed in Cyprinodontidae (Teleostei: Cyprinodontiformes). Zootaxa 4294(5): 573–585. DOI: 10.11646/zootaxa.4294.5.6. Reference page. 
• Freyhof, J., Weissenbacher, A. & Geiger, M. 2017. Aphanius kruppi, a new killifish from Oman with comments on the A. dispar species group (Cyprinodontiformes: Aphaniidae). Zootaxa 4338(3): 557–573. DOI: 10.11646/zootaxa.4338.3.10. Reference page. 
• Mohammadian-Kalat, T., Esmaeili, H.R., Aliabadian, M. & Freyhof, J. 2017. Re-description of Alburnus doriae, with comments on the taxonomic status of A. amirkabiri, A. mossulensis, A. sellal and Petroleuciscus esfahani (Teleostei: Cyprinidae). Zootaxa 4323(4): 487–502. DOI: 10.11646/zootaxa.4323.4.3. Reference page. 
• Tutman, P., Freyhof, J., Dulčić, J., Glamuzina, B. & Geiger, M.F. 2017. Lampetra soljani, a new brook lamprey from the southern Adriatic Sea basin (Petromyzontiformes: Petromyzontidae). Zootaxa 4273(4): 531–548. DOI: 10.11646/zootaxa.4273.4.4. Reference page. 

2018

• Bayçelebi, E., Kaya, C., Turan, D., Ergüden, S.A. & Freyhof, J. 2018. Redescription of Garra turcica from southern Anatolia (Teleostei: Cyprinidae). Zootaxa 4524(2): 227–236. DOI: 10.11646/zootaxa.4524.2.6 Reference page. 
• Brahimi, A., Libois, R., Henrard, A. & Freyhof, J. 2018. Luciobarbus lanigarensis and L. numidiensis, two new species of barbels from the Mediterranean Sea basin in North Africa (Telostei: Cyprinidae). Zootaxa 4433(3): 542–560. DOI: 10.11646/zootaxa.4433.3.9 Reference page. 
• Freyhof, J., Bayçelebi, E. & Geiger, M. 2018. Review of the genus Cobitis in the Middle East, with the description of eight new species (Teleostei: Cobitidae). Zootaxa 4535(1): 1–75. DOI: 10.11646/zootaxa.4535.1.1 Reference page. 
• Freyhof, J., Kaya, C., Bayçelebi, E., Geiger, M. & Turan, D. 2018. Generic assignment of Leuciscus kurui Bogutskaya from the upper Tigris drainage, and a replacement name for Alburnus kurui Mangit & Yerli (Teleostei: Leuciscidae). Zootaxa 4410(1): 113–135. DOI: 10.11646/zootaxa.4410.1.6 Reference page. 
• Freyhof, J., Özuluğ, M., Kaya, C., Bayçelebi, E. & Turan, D. 2018. Redescription of Alburnus kotschyi Steindachner, 1863, with comments on Alburnus sellal adanensis Battalgazi, 1944 (Teleostei: Leuciscidae). Zootaxa 4382(3): 573–582. DOI: 10.11646/zootaxa.4382.3.8 Reference page. 
• Friedrich, T., Wiesner, C., Zangl, L., Daill, D., Freyhof, J. & Koblmüller, S. 2018. Romanogobio skywalkeri, a new gudgeon (Teleostei: Gobionidae) from the upper Mur River, Austria. Zootaxa 4403(2): 336–350. DOI: 10.11646/zootaxa.4403.2.6 Reference page. 
• Gong, Z., Freyhof, J., Wang, J., Liu, M., Liu, F., Lin, P-C., Jiang, Y-L. & Liu, H-Z. 2018. Two new species of Garra (Cypriniformes: Cyprinidae) from the lower Yarlung Tsangpo River drainage in southeastern Tibet, China. Zootaxa 4532(3): 367–384. DOI: 10.11646/zootaxa.4532.3.3 Reference page. 
• Özuluğ, M., Geiger, M.F. & Freyhof, J. 2018. Alburnus goekhani, a new species of bleak from the Anatolian Black Sea basin (Teleostei: Leuciscidae). Zootaxa 4425(1): 29–40. DOI: 10.11646/zootaxa.4425.1.2 Reference page. 
• Turan, D., Kaya, C., Geiger, M. & Freyhof, J. 2018. Barbus anatolicus, a new barbel from the Kızılırmak and Yeşilırmak River drainages in northern Anatolia (Teleostei: Cyprinidae). Zootaxa 4461(4): 539–557. DOI: 10.11646/zootaxa.4461.4.5 Reference page. 
• Yoğurtçuoğlu, B. & Freyhof, J. 2018. Aphanius irregularis, a new killifish from south-western Anatolia (Cyprinodontiformes: Aphaniidae). Zootaxa 4410(2): 319–330. DOI: 10.11646/zootaxa.4410.2.4 Reference page. 

2019

• Freyhof, J., Kaya, C., Bayçelebi, E., Geiger, M. & Turan, D. 2019. Comments on the holotype of Alburnus kurui Mangit & Yerli 2018 and re-description of A. carianorum Freyhof, Kaya, Bayçelebi, Geiger & Turan, 2019 (Teleostei: Leuciscidae). Zootaxa 4550(4): 594–596. DOI: 10.11646/zootaxa.4550.4.10 Reference page. 
• Freyhof, J., Kaya, C., Turan, D. & Geiger, M.F. 2019. Review of the Oxynoemacheilus tigris group with the description of two new species from the Euphrates drainage (Teleostei: Nemacheilidae). Zootaxa 4612(1): 029–057. DOI: 10.11646/zootaxa.4612.1.2. Reference page. 
• Freyhof, J. & Turan, D. 2019. Alburnus magnificus, a new species of bleak from the Orontes River drainage (Teleostei: Leuciscidae). Zootaxa 4559(2): 373–383. DOI: 10.11646/zootaxa.4559.2.10 Reference page. 
• Mousavi-Sabet, H., Vatandoust, S., Geiger, M.F. & Freyhof, J. 2019. Paracobitis abrishamchiani, a new crested loach from the southern Caspian Sea basin (Teleostei: Nemacheilidae). Zootaxa 4545(3): 375–388. DOI: 10.11646/zootaxa.4545.3.3 Reference page.