The phylogeography traditionally correlates the genetic relationships among individuals within a macroorganism species, to their spatial distribution. Most microbial phylogeographic studies so far have been restricted to narrow geographical regions, mainly focusing on isolated strains, either obtained by culture or single-strain natural enrichments. However, the laborious culture-based methodology imposes a low number of studied individuals, leading to poor resolution of haplotype frequency estimation, making difficult a realistic evaluation of the genetic structure of natural microbial populations in the environment. To tackle this limitation, we present a new approach to unravel the phylogeographic patterns of bacteria combining (i) community-wide survey by 16S rRNA gene metabarcoding, (ii) intra-species resolution through the oligotyping method, and (iii) genetic and phylogeographic indices, as well as migration parameters, estimated from populational molecular data as traditionally developed for macroorganisms as models. As a proof-of-concept, we applied this methodology to the bacterial genus Spirochaeta, classically reported as a gut endosymbiont of various invertebrates inhabiting the Southern Ocean (SO), but also described in marine sediment and in open waters. For this purpose, we centered our sampling into three biogeographic provinces of the SO; maritime Antarctica (King George Island), sub-Antarctic Islands (Kerguelen archipelago) and Patagonia in southern South America. Each targeted OTU was characterized by substantial intrapopulation microdiversity, a significant genetic differentiation and a robust phylogeographic structure among the three distant biogeographic provinces. Patterns of gene flow in Spirochaeta populations support the role of the Antarctic Polar Front (APF) as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current (ACC) appears as the main driver of connectivity between geographically distant sub-Antarctic areas such as Patagonia and Kerguelen archipelago, and between Kerguelen archipelago and maritime Antarctica. Additionally, we found that historical processes (drift and dispersal limitation) together govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach represents a substantial first attempt to bridge the gap between microbial and macrobial ecology by unifying the way to study phylogeography. We revealed that strong congruency with macroorganisms patterns at the populational level shaped by the same oceanographic structures and ecological processes.