The seeming lack of barriers to gene flow in the northwest Atlantic ocean has led to the general assumption that the population of the American lobster (Homarus americanus) is largely panmictic. However, morphological and genetic data presented in this dissertation suggest that lobster populations are less homogenous than once believed with potential for behavioral barriers to mating and selection of locally adaptive traits. Additionally, both long-term fishing pressures and the recent spread of a destructive epizootic shell disease may have impacted population structure. We developed a novel photographic technique to rapidly collect accurate morphological data with the ability to maintain a database of images for the purposes of re-sampling and testing additional hypotheses. During this study, we found significant morphometric differences between samples of lobsters from collection sites as close as 25km apart. Morphological differences may have originated due to differential selection or plastic responses to environmental variation. To analyze population genetic structure, I surveyed genetic variation using RADseq. Analysis of 1614 putatively neutral SNPs found little genetic difference (Average F¬ST=0.00137) between sample sites suggesting a high level of gene flow between regions. Several additional markers appeared to be under divergent selection between sample sites. A genome scan analysis of both neutral SNPs and SNPs under selection found several selected SNPs associated with principal components of morphological characters. A subsequent BLAST analysis identified a number of the selected SNPs lying in the H. americanus transcriptome, suggesting functional importance. Further experimentation is required to quantify the impacts of plasticity or local adaption in the origin of morphological differences between lobster populations, although the significant differences identified in this research are likely due to a combination of the two. The overarching conclusion is that lobster populations are, in fact, more differentiated than previously predicted and, as such, the findings presented here may have significant management implications.