Different allozyme genotypes at the mannose phosphate isomerase (Mpi) locus in the northern acorn barnacle (Semibalanus balanoides) show a strong association with distinct intertidal microhabitats. In estuaries along the Maine Coast, the FF homozygote has higher fitness in exposed, high-tide level microhabitats while the SS homozygote has higher fitness under algal cover or at low-tide microhabitats. These patterns are consistent with a Levene (1953) model of balancing selection. In these same samples, polymorphisms at the glucose phosphate isomerase locus (Gpi) and mitochondrial DNA (mtDNA) show no fitness differences among microhabitats, providing intra-genomic controls supporting selection at or near Mpi. Here we report a similar analysis of genotype-by-microhabitat associations at sites in Narragansett Bay, Rhode Island, close to the southern range limit of S. balanoides. Genotype zonation at Mpi between high- and low-tide microhabitats is significantly different between Maine and Narragansett Bay due to opposite zonation patterns for the SF and FF genotypes. Enzyme activity data are consistent with this “reverse” zonation. At Gpi, there is significant microhabitat zonation in Narragansett Bay, while this locus behaves as a neutral marker in Maine. Mt DNA shows no significant microhabitat zonation in either Rhode Island or Maine. The Mpi data suggest that Levene-type selection for alternative genotypes in alternative habitats may operate at scales of both 10's of meters and 100's of kilometers. The Gpi data show how an apparently neutral locus can exhibit non-neutral variation under different environmental conditions. We argue that both Mpi and Gpi provide important genetic variation for adaptation to environmental heterogeneity that is recruited under distinct conditions of stress and carbohydrate substrate availability.