Objective: To evaluate the physico-chemical composition and the presence of potentially useful bacterial to be used as biofertilizer in the excreta of Dendrocygna javanica and Anas platyrhynchos domesticus. Methodology: The microbial culture and physico-chemical analysis was done at the department of botany, Gauhati university. Six different media were taken for microbial growth. After 24 hours of observation microbial colonies were counted and recorded. For physico-chemical analysis four parameters were taken viz., organic carbon, ash content, moisture content and pH, as those four components are essential for soil and plant growth. Findings: The excreta of Dendrocygna javanica show abundant growth of nitrogen fixing bacteria, less fastidious bacteria, yeast, moulds, Acetenomycetes and phosphate solubilizing bacteria. Physico chemical analysis have also shown favourable result against Dendrocygna javanica, indicating the biofertilizer nature of its excreta. Novelty: There is limited literature available concerning the microbial profile and physico chemical analysis of faeces of Dendrocygna javanica and Anas platyrhynchos domesticus. Infect, the present study provided the guidance for culturing and conserving these two duck species since these have a good possibility as bio fertilizers.