Copepods are dominant members of the zooplankton and the most abundant forms of life. Studying the bacterial diversity associated with copepods will helps in understanding the impact of global climate change on these organisms. It is important to address the core microbiome of copepods which has a key role in their host health and ocean biogeochemical cycle. Early studies have identified few bacterial phyla and orders as core microbiome. So to predict the important Operational taxonomic units (OTUs), we used meta-analysis, and machine learning (RandomForest Classifier) approaches. Also, we explore the biogeochemical potential of copepods associated bacteriobiome (CAB). Overall, 50 important s-OTUs were predicted by machine learning; among them, 38 s-OTUs were specific to Calanus spp. and 17 s-OTUs were specific to Acartia spp. Six bacterial genera were identified as important core sub-OTUs in copepods for the first time, i.e. Micrococcus luteus, Krokinobacter eikastus, Vibrio shilonii, Acinetobacter johnsonii Burkholderia and Sphingobium. From the PICRUST2 analysis, the potential genes responsible for methanogenesis (aerobic and anaerobic), methanotrophy and iron fertilization were high in the CAB of Pleuromamma spp.. The potential nitrogen-fixing genes were relatively high in the CAB of Pleuromamma spp.. Whereas the potential genes for denitrification were relatively high in the CAB of Temora spp., and the potential Dissimilatory Nitrate Reduction (DRNA) genes were relatively high in Acartia spp.. All the CAB of the copepod genera investigated in the present study has potential genes for cobalamin synthesis.