Patterns of genetic and phenotypic variations are being of critical importance for the sustainability of the population and the persistence of the species. Genetic diversity correlates with the abundance and size of populations therefore has great ecological significance. As so far, it is not studied in Pakistan, this work was aimed at determining the genetic diversity and population structure for house sparrow across the selected habitats and to document its morphological characteristics. The total number house sparrow captured was 229 from two districts of Punjab (Faisalabad and Rawalpindi) studied for morphological measurements. While the blood samples was able to collect from 193 samples of these. Morphometric data analysis of house sparrow as influenced by site, sub-site and sex of the birds for nice characters ( viz., body weight, wing span, tail length, wing length, wing span and tail length ) revealed significant results. Microsatellite markers (16) were used to determine the genetic relationship among two populations of house sparrow captured from two habitats. The mean observed number of alleles (Na) ranged from 2.81-4.10 (sub-site III for Rawalpindi population to sub-site III for Faisalabad respectively). The Na per locus ranged from 2-8 indicated mean value of 6.75. The values of observed heterozygosity (Ho) ranged from 0.38- 0.51 for sub-site I of Faisalabad to sub-site III of Rawalpindi correspondingly. The deviation from HW equilibrium was 75.78% calculated from locus population comparison. FST (variation due to differences among populations) and FIS (variation within a population) indicated the relative utility of each marker for variations among populations based of allele frequency differences. All loci contributed significantly to the overall differentiation among populations across the sub-habitats of two major habitats (Faisalabad and Rawalpindi). The phylogenetic relation of populations was determined from Nei’s standard genetic distances (Ds) using MEGA software. UPGMA (unweight pair group method for arithmetic means) was used to obtain the phylogenetic tree having two main clusters denoted by “a” and “b”. The topology of UPGMA tree approved well to the history and geographic distribution of house sparrow populations with few atypical results. These results suggested that on small scale the ecological factors have strong influence on morphological and genetic variations as well as on the size of the population. Generally the fragmented environment can cause fine scale patterns of genetic diversity which helps to ascertain factors restraining population size and regulate conservation potential.