During the present study, population estimation was carried out in Cholistan desert and Kalabagh private game reserve area. In Cholistan, the total 41 transects and in Kalabagh game reserve area, 04 transects was surveyed. The mean value of males/transect was 1.200?0.131 in Rahim Yar Khan, 0.381?0.076 in Bahawalpur/Bahawalnagar and 4.250?0.773 in Kalabagh, females/transect was 1.40?0.212 in Rahim Yar Khan, 0.262?0.077 in Bahawalpur/ Bahawalnagar and 7.625?1.322 in Kalabagh, and fawns/transect was 0.680?0.172 in Rahim Yar Khan, 0.119?0.051 in Bahawalpur/ Bahawalnagar and 4.375?0.730 in Kalabagh. The comparison between Cholistan desert and Kalabagh regarding population of Indian gazelles were statistically highly significant (P<0.01). The population density/km2 in Rahim Yar khan was 0.656 animals/km2 and total population was 1770 animals, in Bahawalpur/Bahawalnagar was 0.152 animals/km2 and total population was 3071 animals and in Kalabagh was 3.25 animals/km2 and total population was 191 animals were calculated. The total 30 (11 ?, 19 ?) blood samples in which the mean value of WBCs, RBCs, Hgb, HCT, MCV, MCH, MCHC, platelets, Neutro, lymphocytes, monocytes andeosinophils were calculated. The comparison between male and female showed that WBCs, RBCs, HCT, MCV, HCH, MCHC, Neutro, Lympho, Mono and Eosino were statistically non significant (P>0.05) while, HGB and PLT were statistically significant (P<0.05). The mean value of urea concentration in males and females were statistically highly significant (P<0.01). The mean value of creatinine, total protein, albumin, ALT, calcium and magnesium in males and females were statistically non-significant (P>0.05). To investigate molecular phylogeny and diversity analysis using mitochondrial cytochrome b, cytochrome c and d-loop region, samples were collected from different localities. Gene amplification was done by polymerase chain reaction after DNA extraction and quantification,. Bi-directional sequencing of PCR products was done and aligned to identify single nucleotide polymorphisms. Bioinformatics tools were applied for formation of phylogenetic tree and genetic diversity analysis. The finding of current study is helpful for future conservation and captive breeding programs of this species.