Unusually for a marine fish clade, most New Zealand triplefin species display broad, sympatric geographic distributions. Explaining diversification in this species flock therefore requires a detailed understanding of patterns of gene flow. Here, we test the patterns reported in previous studies by examining population structure over a range of spatial scales in Forsterygion lapillum and at regional scales in F. capito using microsatellites. Samples were collected between 2000 and 2009, and between 35°56′S and 46°36′S. The microsatellite findings differ from previous mtDNA results in several key respects. First, there is no support for a genetically distinct population at Banks Peninsula, as was seen with mtDNA. Second, in contrast to mtDNA, the two triplefin species exhibited very similar patterns of population structuring at regional scales (102–103 km), suggesting that year-round spawning only in F. lapillum does not have a significant effect on population connectivity. Third, while there is evidence of isolation by distance in both species, there are no clear phylogeographic breaks, and far less structure is evident than in the mtDNA data. Further, we found a lack of structure over local scales in F. lapillum, suggesting extensive gene flow over tens of kilometres. Our findings suggest a pattern of stepping-stone dispersal and contiguous gene flow, sometimes over large distances, supporting the hypothesis that factors other than geographic isolation, such as ecological speciation with gene flow, have been important in the evolution of this group.