The interaction between selection and gene flow can determine to what degree populations are able to adapt to local environmental conditions. This presents a particular conundrum in marine systems, as many marine species have high dispersal capacity resulting in nearly panmictic populations. Increasingly, genomic studies find that even in systems with little or no population structure divergence at particular loci may indicate local adaptation in the presence of high gene flow. However we are just beginning to understand which environmental variables might be the strongest drivers of selection in marine systems and the functional outcomes of genetic variants that are candidates for selection. Here, we leverage fine-scale sampling across the California range of the Pacific Purple Urchin (Strongylocentrutus purpuratus), a species with previous evidence of both local adaptation and extremely high gene flow. We find that despite complete absence of neutral population structure, sea surface temperature and tidal height drive genetic differences among populations, suggesting that balanced polymorphisms can lead to adaptation across both large scale (latitudinal) and small scale (subtidal v. intertidal) scales. Further, we find that genes that are expressed at a single tissue or life history stage are more divergent than expected across both latitudinal and tidal height comparisons, suggesting that these genes have specific functions that might generate phenotypic variation important for local adaptation. Together these results suggest that even in panmictic populations genetic variation can be sorted across even small spatial scales, potentially resulting in local adaptation across a complex environmental mosaic.