Newly established populations are susceptible to founder events that reduce genetic variation. This may be counterbalanced by gene flow after populations become established or founders coming from genetically different populations. However, initial gains in genetic diversity may be short-lived if there is limited mixing between lineages and subsequent inbreeding, or if one lineage sweeps to fixation through selection or genetic drift. Here, we report on the genetic changes taking place within two newly established populations of intertidal snail over a 15-year period (∼ 10 generations). Each translocation was set up using multiple, genetically distinct source populations. Our data show that higher levels of variation in the translocated populations compared to the source populations were maintained over time for both nuclear (microsatellite) and mitochondrial genes. Small changes in allele and haplotype frequencies were observed in the source populations and in one of the translocated populations, but marked changes were evident in the other, where there was a dramatic shift towards the genetic make-up of one of the source populations. These genetic changes occurred despite relatively large numbers of founders (200–374 adults) and no evidence of the population experiencing a severe reduction in effective population size. Our study shows that the genetic composition of newly established populations can vary greatly over time and that genetic outcomes can be highly variable, and significantly different from initial expectations, even when they are established using high numbers of individuals and involve source populations from the same geographic regions.