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The use of polymorphic gene markers is a widely used alternative to traditional methods of trait selection in livestock. This study aims to determine the polymorphism of three milk gene markers: κ-casein, β-casein, and β-lactoglobulin in the Siquijor native (SN, n=124) and Holstein x Sahiwal (HS, n=86) cattle. Genotyping was done primarily by PCR-RFLP analysis while PCR-sequencing was followed only for the β-casein of the SN herd. Results showed that for the β-lactoglobulin, the genotypic frequencies of AA, AB, and BB in the HS were 0.174, 0.464, and 0.362, whereas in the SN these were 0.025, 0.099, and 0.876 respectively. The distribution of κ-casein genotypes was 0.589, 0.286, and 0.125 for the AA, AB, and BB genotypes for the HS respectively, and 0.442, 0.425, and 0.133 for the SN. β-casein genotypes showed that the A1A1, A1A2, and A2A2 were 0.143, 0.755, and 0.102 respectively in the HS and 0.600, 0.320, and 0.080 in the SN. Our results show that the three genes are polymorphic in the SN and HS cattle. It is recommended to conduct an association study between these polymorphic variants and milk quality traits to confirm their usability as gene markers for future selection. [ABSTRACT FROM AUTHOR]