Microorganisms in breeding sites may act as important factors for attracting or repelling mosquitoes. This study investigated the presence and counts of bacteria and fungi isolates from mosquito breeding sites in Eziobodo Community of Owerri West Local Government Area of Imo State, Nigeria. The work was carried out by collecting 5 water samples each from randomly selected breeding site types in the study area. Microbial analysis of the water samples were done using culture, microscopy and biochemical techniques. The breeding sites identified in the study include Tireopenings, ground puddles, Generator house area, and open containers. The bacteria isolated were Bacillus sp, Acinetobacter sp, Staphylococcus sp, Pseudomonas sp, Escherichia coli, and Klebsiella spwhile the fungi isolated were Aspergillus flavus, Aspergillus niger, Aspergillus fumigatus and Candida sp. Acinetobacter sp showed the highest counts in ground puddles and open containers, Staphylococcus sp showed highest counts in Tire openings whereas, in Generator houses only staphylococcus sp and Escherichia coli were the only bacteria isolated. Awareness on the importance of environmental management among residents in the control of mosquitoes as well as disruption of microbial activities in breeding sitescould be included in current measures to control mosquito vector borne diseases in the study area.