Idotea balthica has long been studied for intraspecific variation at the phenotypic and ecological level. Recent work found deep genetic divergences among several regional populations of this species in the North Atlantic. Here we report development of microsatellite loci for Idotea and use these newly developed markers to evaluate population structure among the mitochondrial clades. We also provide a detailed morphological evaluation, including SEM description of relevant traits in one of the more divergent groups. Phenotypically, the examined clades do not differ significantly, though individuals from populations in Virginia (U.S.A.) have more setose pereiopods than European and other museum specimens. The preliminary microsatellite data presented here suggest that these markers should be of utility for a variety of small-scale ecological and behavioral analysis in some related Idotea species. Although microsatellites are inappropriate for species designations, there is significant differentiation among mitochondrial lineages indicating that nuclear loci may show similar differentiation as mtDNA among regions. Together the subtle morphological variation and microsatellite data suggest that additional nuclear gene sequencing and reproductive studies are warranted to determine the taxonomic status of these regional forms.