We predict estuaries to be hotspots of hybridisation between migratory marine and estuary-restricted species, although hybridisation rates may vary in space and time, reflecting the dynamic nature of estuaries and potentially widespread but erratic dispersal of marine taxa. Within estuaries, genotype frequencies may reflect past hybridisation events, with genetically intermediate and backcrossed individuals contributing to persistent hybrid swarms. In southeastern Australia, hybridisation has occurred between estuarine black bream Acanthopagrus butcheri and marine yellowfin bream A. australis, but it is unclear whether this reflects a contemporary process. We recently found that, within lakes and lagoons at the southern range limit of A. australis, hybrids were abundant and A. butcheri extremely rare, and surprisingly, we detected hybrids within a small sample of fish from the Gippsland Lakes, an estuary 250 km further south. In the present study, we compare the genotypic composition of the contemporary Gippsland Lakes population of Acanthopagrus spp. with the historical composition revealed by analysis of museum specimens. The genetic makeup of samples varied little over time, with ancestral A. butcheri virtually absent, and most introgressed individuals matching expectation for later-generation hybrids or A. butcheri backcrosses, suggesting that the lakes have supported persistent hybrid swarms. At each sampling time, the samples were genetically diverse, as measured by mean number of alleles per locus, which ranged from 8.2 to 9.2, and expected heterozygosity (He), which ranged from 0.66 to 0.70; however, we detected little allelic differentiation (FST= 0.003) across sampling times. Our data imply that introgressed populations of Acanthopagrus spp. are more widespread and persistent than previously predicted.