Global environmental change is rapidly driving deterioration of many ecosystems- such as coral reefs- though the rate of decline could be offset by genetic adaptation. We aimed to identify which environmental gradients drive local adaptation in two common corals across the Florida Keys Reef Tract, Porites astreoides and Agaricia agaricites. Both species contained three genetically distinct lineages distributed across depths in a remarkably similar way. Additionally, each lineage harbored genetic variation that aligned with other environmental gradients. The most commonly highlighted driver of within-lineage genetic structure was temperature during the coldest winter month, which is warmer at offshore sites especially in the upper Keys. Other repeatedly highlighted environmental drivers were high variation in bottom temperature at nearshore sites along the main island chain, more pronounced ocean stratification west of Key West, and outlying values of several water quality parameters (such as dissolved oxygen, carbon, turbidity, and salinity) at nearshore and Florida Bay locations of the lower and middle Keys. Synthesizing these results, we provide a map of adaptive neighborhoods in the Florida Keys that are likely to harbor differentially adapted coral populations, which can be regarded as different genetic stocks from the perspective of reef conservation and restoration.