Cobitis species exist in both diploid and diploid-polyploid (d-p) populations, but mostly occur in the latter. They are considered an important model organism to study the biology and physiology of natural hybrid and polyploid vertebrates. Indeed, polyploidization causes a huge stress for in terms of cell physiology and alters spermatogenesis in polyploid fish. The most extensively studied mode of germ cell death during spermatogenesis in vertebrates is apoptosis. The aim of this study was to examine caspase-3 immunoexpression in the testes of Cobitis taenia from a diploid population as well as C. taenia and sterile tetraploid Cobitis from d-p populations before, during and after spawning. The obtained results suggest a different performance of apoptosis in the testes of C. taenia from the two studied populations and seems to be conditioned by their role as the only sperm donors in d-p populations. Moreover, apoptosis was an active cell death process in the testes of tetraploid Cobitis.