Delimiting species boundaries in recent plant radiations can be challenging. The New Zealand native Myosotis pygmaea (Boraginaceae) species group is a case in point. This species complex is of interest as it includes threatened species as well as possibly threatened unnamed putative taxa. Integrative taxonomic approaches using multiple lines of evidence are frequently used to overcome the difficulties of identifying lineages resulting from recent radiations. Here we analyse genotypic data from nearly 500 Myosotis individuals using microsatellite markers, and compare and co-analyse this dataset with previously published morphological data. Within the M. pygmaea group, several genetic clusters can be identified, none of which align exactly with the current taxonomy and morphological variation previously identified. When co-analysing the molecular and morphological data, M. brevis can be distinguished from the remainder of the M. pygmaea species group, but no other species or previously recognised morphological groups are supported. Other groupings within the molecular dataset appear to reflect geographic structure. Within the M. pygmaea species group, the resulting pattern of low within, and high between, population genetic variation is consistent with self-fertilization and low levels of seed dispersal.