The subterranean caves represent one of the most suitable examples of extremities in ecosystem and the microbes abiding in such environments represent truly extremophiles in nature. In the present study, Micrococcus bacterial strains were isolated from various depths of the Kotumsar cave (India) and further 12 strains of 3 specific species (M. luteus, M. radiodurans and M. agilis) have been selected for further studies. The protein profiles by SDS-PAGE technique were estimated for each strain and the effect of subterranean depth on the characterization of protein profiles have been tried to establish by the linear regression method. The strains isolated from the deeper zones of the cave exhibits more number of protein bands, carrying higher molecular weights. Statistical analysis also support the same i.e., the strains isolated from the deeper zones of the cave revealed much protein as compared to the strains isolated from the anterior zones. The chances of developing extremozymes (biocatalysts) in the strains, isolated from the deeper zones could not be denied. Further, the result obtained from this study also suggests redrawing the evolutionary tree of studied bacterial strains.