Freshwater fish of the genus Carassius are widely spread in Asia, Europe, and Australia. This includes the Carassius auratus complex, a phylogenetically diverse species complex with uncertain taxonomy. The C. auratus complex is native to Asia but has been introduced to non-native habitats. It includes s diploid as well as polyploidy individuals. The evolutionary relationship between the different reproductive modes as well as the invasion history of different lineages are poorly understood. A phylogenetic approach using mitochondrial DNA Cyt b sequences in combination with six microsatellites markers was used to investigate the invasion history of different lineages and reproductive modes and to understand the evolutionary relationship between different reproductive modes. The Cyt b analysis was based on sequences from native populations and invasive populations. Furthermore, 1427 individuals were genotyped at six microsatellite loci to determine their level of ploidy. Furthermore, phylogenies of three nuclear genes were used to test the origin of triploid lineages. We suggest that the invasion of C. auratus complex in Europe went through two routes, one could have been driven by historical and anthropogenic events. The microsatellite analysis revealed 67.19% triploids and 33.8% diploids. Interestingly, most of native populations consisted of a mixed of diploids and triploids but were dominated by triploid. While invasive populations showed a considerable variety in reproductive mode ranging from purely diploid to purely triploid and mixed populations. Additionally, diploids are dominant in older Eastern European populations whereas triploids are dominant in more recently established in Central European populations. The C. auratus complex provides an ideal model for studying the reproductive traits of polyploids, which is of great value in animal genetics and reproductive biology.