Despite the key roles of microorganisms in the Southern Ocean (SO) in organic matter transformation, nutrient re-generation, and biogeochemical cycling, the microbial communities in East Antarctica remain poorly understood. Thus, we integrated metagenomic and public data to characterise surface microbial communities in the Cosmonaut and Cooperation Seas (CCS), specifically comparing their composition, functional traits, and potential changes with those of microbes in other SO sectors. CCS was characterised by a markedly different microbial community composition and higher microbial diversity. Niche analysis indicated that SO surface communities were shaped primarily by environmental filtering, whereas CCS harboured a higher proportion of generalists and a lower proportion of specialists. Genome-resolved analyses demonstrated that the regional signature of CCS was supported by multiple phylogenetic lineages and associated with a functional configuration characterised by resource acquisition, cold adaptation, and auxiliary energy utilisation. The findings further suggested that global warming will intensify community re-organisation, reduce inter-regional community differentiation, and weaken the core lineages and resource-acquisition functions that currently underpin CCS-specific characteristics. This study provides new insights into microbial ecological processes and their potential functional shifts in East Antarctic marginal seas.