The invasiveness presented in the history of Carassius gibelio species as well as the current economic and ecological importance is still making this species an important object of study. The mobility degree of fish is determined by physicochemical parameters of the aquatic environment and by the interconnectivity of watershed. The gene flow and the genetic diversity of populations are directly correlated by this mobility degree. A geographical isolation of a population leaves their marks on the genetic fund and can dictate certain development directions of individuals in order to allow their adaptation to the new environmental conditions. Due to the presence of specific pathogens in different aquatic habitats and the presence or absence of gene flow between populations, the responsible immunity genes for individuals may be modified, defining different haplotypes between populations from specific environments. The aim of this study was to highlight the differences between Carassius gibelio individuals sampled among the Danube basin, from various aquatic habitats. Using a genetic approach, we had analyzed Carassius gibelio samples collected from the Bistrița River and a nearby lake and also samples from different Romanian lakes and rivers. For this study we analyzed one mitochondrial gene (cytochrome b) and one nuclear gene (MHC class II). All sequences were aligned using ClustaW method in MEGA 7 software. Phylogenetic trees were constructed using SeaView 4, the optimum substitution model was identified using jModelTest 2.1.4. and the visualization of the trees was performed in FigTreev.1.4. software. The mapping of MHC class II gene revealed the differences between individuals originating from different aquatic environments, as punctual mutations and block insertions of nucleotides. The phylogenetic tree obtained by analyzing the cytochrome b sequences of individuals from Danube basin is showing a common ancestor and also a specific clustering of the majority individuals from the Bistrița River.