Molecular identification of animals is becoming increasingly important to preserve and maintain pure breeds worldwide. The issue is aggravated with rise in import of foreign animals and germplasm in Pakistan. It is becoming difficult to find pure males of Sahiwal breed for breeding purpose in public as well as private semen production units. The present study was designed to develop standard molecular markers for Sahiwal to ascertain their purity for breeding purpose. In this study, 50 and 48 unrelated males were sampled for each Sahiwal and Crossbred cattle respectively. Candidate molecular markers present in Sahiwal but absent in Crossbred and vice versa were detected using amplified fragment length polymorphism (AFLP) method. Eleven markers were developed that were converted to SNP markers for genotyping. The allele frequencies in both breeds were determined for discrimination ability using AFLP. Data were analyzed using Arlequin 3.5. The probability of identifying Sahiwal breed was 0.86 and probability of misjudgment was 0.021 using single selected markers. However, probabilities for judgment and misjudgment with 2 markers and combined with 3 markers were 0.745, 0.367 and 0.964, 0.376 respectively. Sahiwal breed and crossbred could be tested using the given markers and can be verified for purity before entering into breeding program.