Thirty-five Anatolian water buffalo were selected from among a total of almost 7000 animals from 11 herds in the Kızılırmak Delta, which is known to be one of the most important areas for water buffalo farming in Turkey. The cleaved amplified polymorphic sequences (CAPS) method was used to identify single-nucleotide polymorphisms at 3 loci that are associated with milk production, namely PRL, CSN3, and PIT-1, which are associated with milk processing and milk yields, respectively. Sequence-tagged sites of PRL, CSN3, and PIT-1 were digested by restriction endonucleases RsaI, HindIII, and HinfI, respectively. Capillary electrophoretic analysis identified all samples as belonging to the GG and BB genotypes, which are undesirable genotypes for PRL and PIT-1 gene loci, but ideal for the CSN3 locus. Then the samples were sequenced by an ABI 3730 DNA Analyzer (Applied Biosystems). DNA sequencing of the amplified CSN3 fragment revealed one polymorphism at codon 135 (ThrACC > IleATC) in some samples. A homozygous structure was found for all three loci and the huge population loss between 1991 and 2008 suggests that a genetic bottleneck may have occurred in the population of Anatolian water buffalo in the Kızılırmak Delta.