© International Council for the Exploration of the Sea 2015. Ocean acidification (OA), caused by seawater CO2 uptake, has significant impacts on marine calcifying organisms and phototrophs. However, the response of bacterial communities, who play a crucial role in marine biogeochemical cycling, to OA is still not well understood. Previous studies have shown that the diversity and structure of microbial communities change undeterminably with elevated pCO2. Here, novel phylogenetic molecular ecological networks (pMENs) were employed to investigate the interactions of native bacterial communities in response to OA in the Arctic Ocean through a mesocosm experiment. The pMENs results were in line with the null hypothesis that elevated pCO2/pH does not affect biogeochemistry processes. The number of nodes within the pMENs and the connectivity of the bacterial communities were similar, despite increased pCO2 concentrations. Our results indicate that elevated pCO2 did not significantly affect microbial community structure and succession in the Arctic Ocean, suggesting bacterioplankton community resilience to elevated pCO2. The competitive interactions among the native bacterioplankton, as well as the modular community structure, may contribute to this resilience. This pMENs-based investigation of the interactions among microbial community members at different pCO2 concentrations provides a new insight into our understanding of how OA affects the microbial community.