Hybridisation is a commonly reported phenomenon in fish. This study focuses on cyprinid species, Cyprinus carpio and Carassius gibelio and their hybrids including F1, F2 and backcross generations obtained by artificial breeding with the aim to investigate the effect of the various types of crossbreeding representing different genomic contribution of common carp and gibel carp on the health and histoarchitecture of key organs involved in metabolism and immunity – the liver and spleen. Comparative histology revealed that there is no clear trend in the organisation of liver and spleen parenchyma based on the type of cross representing the differential genomic contribution of common carp and gibel carp. However, there are similarities between certain fish lines, most noticeable in the specific properties of hepatocytes and in the pattern of glycogen distribution in their cytoplasm, and in the organisation of splenic fibrous skeleton. Moreover, this study suggests that long-term breeding of wild fish species in artificial conditions can affect their physiology, as we noted extravascular haemolysis affecting parts of the splenic parenchyma and small foci of hepatic necrosis. Compared to gibel carp and hybrid lines, the common carp with a longer history of cultivation showed he mildest forms of the pathologies detected, indicating that it coped best with the conditions of artificial breeding.