Turkish grey cattle (TGC) are facing the danger of extinction. Intensive breeding program has mainly been used for purebred TGC that are under the conservation of Bandırma Livestock Research Institute (BLRE) ex-situ program. This study aims to compare 3 SNP of the genetic features of purebred TGC that are under the conservation of ex-situ (51 cattle) program with the ones raised by the smallholders (79 cattle) in the villages. According to the estimated average heterozygosity values for ex-situ breeding program and smallholders in the villages, the difference between the cattle were found meaningful (P<0.05). The observed average heterozygosity (Ho) value was calculated as 0.4077±0.1922, while the expected heterozygosity (He) value was found 0.3909±0.1663. The research findings show that the difference between the two TGC groups in terms of Calpastatin gene (CAST) loci (P<0.01) and Calpain gene (CAPN1) loci (P<0.05), gene assortment was found to be meaningful and these are incompatible along with Hardy-Weinberg theory. In addition, significance check was done for the expected heterozygosity results for the two TGC groups (BLRE ex-situ and the smallholders in the villages). For the Fis value, the difference was significant for CAPN1 316 loci (P<0.001) and CAST loci (P<0.05) and non-balanced but the CAPN1 4751 loci (P>0.05) which did not display a significant difference. The Fis inbreeding coefficients being negative in the sample populations for CAST loci imply heterogeneity in CAST loci (P<0.001). The effective allele number and allele density are other criteria to show the spatial heterogeneity in a population. The average effective allele number (ne) per loci for TGC samples from the smallholders in the villages, TGC ex-situ conservation herd and the total population sample were calculated as 1.7379±0.3559, 1.6026±0.4422 and 1.7103±0.4018, respectively.