The future bio-economy of dairy industry relies on the identification of an affordable approach for increasing milk production and its constituents. Egyptian buffalo (Bubalus bubalis) contributes by about 50% of total milk production in Egypt, therefore it is considered as an essential dairy animal. This study aimed to differentiate between high and low milk producer buffaloes (Bubalus bubalis) using microsatellite and SCoT markers. The results of the six microsatellite primers showed bands of 350, 377, 496, 247, 262 and 280 bp, where three of which were digested by restriction enzyme. SCoT results of bulked samples showed unique bands that were sequenced and aligned to Bubalus bubalis (taxid: 89462) sequences. Alignment results showed similarity to the following encoding genes, Class V myosin, Ubiquitin-conjugating enzyme E2 D4 and acyl-phosphatase 2 (ACYP2), which play a crucial role in organelle trafficking and many pathways, that may affect milk production traits. These results showed that SCoT marker was better than microsatellite in clarifying the difference between high and low milk producing traits in Egyptian buffalo (Bubalus bubalis).