The SE Baltic region harbors a diverse assemblage of alien amphipods of Ponto-Caspian origin. The composition of this fauna was shaped by three invasion waves: (1) pre-twentieth century dispersals via watershed-connecting canals, (2) deliberate introductions in the 1960s, and (3) last decade dispersals via shipping and existing canals. Given this complex history, we test whether genetic diversity (mitochondrial COI and nuclear OPS) differs between the native and invaded ranges and between the deliberately introduced species and the ones that dispersed on their own. We find that in the native range the two species groups exhibited similar COI diversity, while OPS diversity was higher in the deliberately introduced species. In the invaded range, COI diversity significantly decreased in all species, but more so in the self-dispersed group. No change in OPS diversity was detected among ranges. Mitochondrial diversity was more structured geographically in the native range, and the dominant invasive haplotypes were detected in the native populations of all but one species, further highlighting the utility of this marker in tracing invasion sources. Our comparative approach provides important insight into the inter-range genetic diversity of Ponto-Caspian invaders, highlighting the role of introduction mode.