Microbial communities are major drivers of global elemental cycles in the oceans due to their high abundance and enormous taxonomic and functional diversity. Recent studies assessed microbial taxonomic and functional biogeography in global oceans but microbial functional biogeography remains poorly studied. Here we show that in the near-surface Atlantic and Southern Ocean between 62°S and 47°N microbial communities exhibit distinct taxonomic and functional adaptations to regional environmental conditions. Richness and diversity showed maxima around 40° latitude and intermediate temperatures, especially in functional genes (KEGG-orthologues, KOs) and gene profiles. A cluster analysis yielded three clusters of KOs but five clusters of genes differing in the abundance of genes involved in nutrient and energy acquisition. Gene profiles showed much higher distance-decay rates than KO and taxonomic profiles. Biotic factors were identified as highly influential in explaining the observed patterns in the functional profiles, whereas temperature and biogeographic province mainly explained the observed taxonomic patterns. Our results thus indicate fine-tuned genetic adaptions of microbial communities to regional biotic and environmental conditions in the Atlantic and Southern Ocean.