Abstract In this study, a total of 53 taxa were identified from 13 catchments in Turkey. Gomphonema affine var. rhombicum E.Reichardt, G. angusticephalum E.Reichardt & Lange-Bertalot, G. calcifugum Lange-Bertalot & E.Reichardt, G. elegantissimum E.Reichardt & Lange-Bertalot, G. exilissimum (Grunow) Lange-Bertalot & E.Reichardt, G. graciledictum E.Reichardt, G. italicum var. densistriatum Levkov, Mitic-Kopanja & E.Reichardt, G. linearoides Levkov, G. megolobrebissonii D.A.Chudaev, Kociolek & M.A.Golobova, G. minusculum Krasske, G. minutum f. syriacum Lange-Bertalot & Reichardt, G. reediae Levkov, Mitic-Kopanja & E.Reichardt, G. sarcophagus W.Gregory, G. subcapitatum (Grunow) E.Reichardt & Levkov and Gomphosphenia holmquistii (Foged) Lange-Bertalot were recorded for the first time in Turkey. Of the identified taxa, Didymosphenia geminata (Lyngbye) M.Schmidt, Gomphonema acuminatum Ehrenberg, G. affine Kützing, G. angustatum (Kützing) Rabenhorst, G. augur Ehrenberg, G. micropus Kützing, G. minutum (C.Agardh) C.Agardh, G. olivaceum (Hornemann) Brébisson, G. parvulum (Kützing) Kützing and G. truncatum Ehrenberg are common in the waters. G. angustius E.Reichardt, G. insignaffine Reichardt, G. insigne W.Gregory, G. italicum Kützing, G. laticollum E.Reichardt, G. pumilum var. rigidum E.Reichardt & Lange-Bertalot, G. stonei E.Reichardt, G. supertergestinum E.Reichardt and G. vibrio Ehrenberg have been recently recorded from the Turkish waters. The genus Gomphosphenia in Turkey has so far been represented only by G. grovei (M.Schmidt) Lange-Bertalot.