Zoometrical index can be used to evaluate the performance of cattle. The present study aimed to detect the genetic markers for zoometrical index of cattle. Forty-five heads of mixed-sex cattle consisting of Bali (16), Madura (16), and Peranakan Ongole / PO (13) were collected from the breeding station for the experimental animals in this study. A Bovine 50K SNP BeadChip was used to explore genetic mutation in the autosomal chromosomes. Nine parameters of zoometrical index were evaluated in the present study. A TASSEL 5.0 software was used to evaluate 24,347 SNP markers. Research showed that two SNP Markers of ARS-BFGL-NGS-115374 (SNP1) and Hapmap28985-BTA-73836 (SNP2) had a significant association with zoometrical index in pool animals based on the Manhattan plot. The SNP1 had a significant association with the area index. Subsequently, a SNP2 significantly correlated with body ratio and over-increase index parameters. In addition, SNP1 is not located in the gene region. Meanwhile, SNP2 is located at the intron 5 region of the Cryptochromes circadian regulator 1 (CRY1) gene. However, this gene was polymorphic in Bos indicus cattle (Madura and PO). In conclusion, the CRY1 gene can improve the zoometrical index in Indonesian Bos indicus cattle (Madura and PO)