The microbial inhabitants of deep-sea vents are genetically and metabolically diverse, and often make a living at the edge of biological temperature limits. Guaymas Basin, a nascent spreading center in the Gulf of California, provides a unique environment in which to study prokaryotic communities across a range of thermal and geochemical niches. Unlike most vents, Guaymas is blanketed in thick sediments, ranging from 3ºC to 200+ºC within half a meter below the sea floor. Microbial mats, including one nicknamed "Megamat," serve as bull's-eyes for subsurface hydrothermal activity. Here we explore Megamat's subsurface, spanning low-temperature (3º), low-methane (0.3mM) to high-temperature (85º), high-methane (3+ mM) sediments, and the 16S rRNA-based phylogeny of active prokaryotes therein. Pyrosequencing revealed the fewest OTUs yet highest Shannon-Wiener diversity within the hottest sediments. Sequences of Sulfurimonas were nearly ubiquitous, and sequences from the heterotrophic MBGB dominated outside the mat's perimeter. Putative methane cyclers were most abundant within the methane-saturated mat center, including ANME-2c, Methermicoccaceae, Guaymas-specific ANME-1 groups, and a deeply-branching, novel group, "Guaymas Methanomicrobia." The expected Deltaproteobacterial sulfate reducers were not common in this survey; in fact Archaeoglobus and Thermodesulfobacteria sequences were recovered in exponentially higher abundance in the hottest sediments. Major groups were most similar outside of Megamat and at its edge, in contrast with strikingly core-specific communities in central mat samples. The mat's edge appears to be a transition zone hosting sequences found both in the central mat and in bare sediment, while the distinct community assemblages within central Megamat highlight horizontal and vertical variability in Guaymas Basin. Together, these data provide insights into community changes with temperature and substrates at high resolution over small spatial scales.