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