A study on ecological preference of breeding sites of Anopheles gambiae compared to other mosquito species were carried out in small natural microcosms. A total of sixteen small ponds, four each from North, South, East and West of Maiduguri Metropolitan were surveyed for the breeding and nonbreeding sites for mosquitoes. In each pond mosquito larvae samples were collected by dip method after identifying species by their angular positions and later confirmed by Polymerase Chain Reaction (PCR). Water samples from which collection of A. gambiae and non-Anopheles gambiae larvae were also collected and analyzed for physico-chemical properties following the standard laboratory procedures. The results revealed that, preference of breeding site of A. gambiae is dependent on the physico-chemical nature of water habitat. Of a total of 30 parameters analyzed, pairwise comparison using SPSS software revealed that 11of the physico-chemical parameters significantly varied (P<0.05) between A. gambiae and non-A. gambiae breeding sites.