Understanding genetic diversity and population structure is essential for the sustainable management of freshwater fish, particularly in systems influenced by long-term stocking. In this context, the genetic status of Albanian common carp (Cyprinus carpio) remains poorly understood. Here, 125 individuals from five populations representing natural lakes (Ohrid and Shkodra), semi-managed freshwater systems (Prespa and Belshi), and a hatchery stock (Tapiza) were genotyped at 12 polymorphic microsatellite loci. High genetic diversity was detected across all populations, with low genetic differentiation and relevant estimates of gene flow. Bayesian clustering identified two main genetic groups, with natural lake populations predominantly represented by a single genetic lineage and managed systems showing higher admixture. Multivariate and phylogenetic analyses supported a close genetic relationship between Ohrid and Shkodra natural lake populations. These patterns may reflect historical stocking and translocation programmes, potentially involving genetically similar or shared broodstock sources, which may have contributed to the observed genetic similarity among populations while maintaining high levels of within-population genetic diversity. The more homogeneous genetic composition of natural lake populations may also reflect local environmental conditions that influenced the distribution of allelic variants among populations. Overall, this study provides a comprehensive genetic assessment of Albanian common carp and establishes a baseline for future sustainable management plans.