Biological invasions are part of processes connected with human activities, which threaten biodiversity and all ecosystems, including freshwaters. Many research studies aim to discover the main traits responsible for invasive success. The topmouth gudgeon is one of the most successful invasive fish species; thus, this study aimed to analyse morphological variability and sexual dimorphism of two topmouth gudgeon populations coming from different sites in Bulgaria (n = 150 in both cases) and to evaluate its morphological variability in connection to differently disturbed habitats of occurrence. For this, we measured thirty morphometric characters, which were subsequently statistically analysed. The species is characterised by high morphological variability between the populations from different sites and also within populations. We showed that populations from Bulgaria differed mainly in traits connected with specific body dimensions. The population from the Kolarovo channel showed a significantly deeper head, bigger mouth and longer body in the front part. On the other hand, the population from Lake Zafirovo had a significantly longer caudal peduncle and caudal and anal fins. Differences between males and females were found between traits connected to the head and fins, which made males more robust with longer fins. At the same time, females were characterised by deeper bodies, which is essential for their investment in reproduction.