The soil sample and earthworm midden collected from agro-ecosystem were analyzed for ecobiological and bioinformatic study. The initial bacterial population (number/g soil) in soil was 36.3±1.50 X109 which significantly increased to 51.1±1.35 X109 (p< 0.01) in earthworm midden (on 0 day). A sharp decline in bacterial population was observed till 42nd day of observation. Microbial population was higher (60.78%) in midden than soil sample (42nd day). Bacterium isolated from earthworm middens from agro-ecosystem, on the basis of genomic analysis using 16s rDNA probe and PCR amplicon a band of 1500bp was identified as Kocuria sp HO-9042 having highest population in midden which is closely related to Kocuria rosea strain and Kocuria sp. RM1 as revealed by BLAST. In the distribution of 100 blast hits on the query sequence of 1500 bp matched the alignment scores≥ 200. Sequence producing significant alignments by BLAST closely matched to Kocuria sp HO-9042, and 10 different strains of Kocuria spp were also found to be close to this species. Expectation value of all these strains was 0.0 which depicts that all the strains are homogenous to Kocuria sp HO-9042. Kocuria spp have been reported to possess hydrocarbon degrading capabilities and considered to the major agents for remediation of contaminated soil. The paper deals in detail the ecobiology and some aspects of bioinformatic study of bacterial species which was found in midden but absent in soil.