Modern　molecular　interventions　are　dynamic　gears　for　breeding　animals　with　superior　genetic　make-up.　These　scientific　efforts　lead　us　toward　sustainable　dairy　herds　with　improved　milk　production　in　terms　of　yield　and　quality.　Many　of　candidate　genes　have　been　dissected　at　molecular　level,　and　suitable　genetic　markers　have　been　identified　in　cattle,　but　this　work　has　not　been　validated　in　buffaloes　so　far.　Stearoyl-coenzyme　A　desaturase　(SCD)　has　been　a　potential　candidate　gene　for　fat　content　of　milk.　Genomic　analysis　of　SCD　revealed　a　total　of　six　variations　that　were　identified　through　DNA　sequencing　of　animals　with　lower　and　higher　butter　fat　%age.　After　statistical　analysis,　genotype　AB　of　p.K158I　could　be　associated　(P　value　＜　0.0001)　with　higher　milk　fat　%age　(10.5　+/-　0.5464).　This　SNP　was　validated　on　larger　data　set　by　cleaved　amplified　polymorphic　sequences　(CAPS)　by　using　DdeI.　To　scrutinize　the　functional　consequences　of　p.K158I,　3D　protein　structure　of　SCD　was　predicted　by　homology　modeling　and　this　variation　was　found　located　in　the　vicinity　of　functional　domain　and　a　part　of　transmembrane　helix　of　this　membrane　integrated　protein.　This　is　a　first　report　toward　genetic　screening　of　SCD　gene　at　molecular　level　in　buffalo.　This　report　illustrates　the　implication　of　SCD　gene　and　in　particular　p.K158I　variation,　in　imparting　its　effect　on　milk　fat　%age,　which　can　be　targeted　in　selection　of　superior　dairy　buffaloes.