Several human health problems have been related to the allergenic constitution of bovine milk due to the body’s immune reaction to milk proteins. It is necessary find solutions to minimize the occurrence of such reactions, given the importance of milk as a source of animal protein. The aim of this study was to evaluate the allelic frequency of the CSN2 gene and to evaluate differences in the characteristics of Gir and Guzerá bovine milk. One hundred and fifty-six cows were used (68 Gir and 88 Guzerá) from the Felipe Camarão Experimental Station herd of the Agricultural Research Corporation of RN (EMPARN). DNA extractions were carried out from hair follicles of the animals; the gene was then amplified and sequenced in an ABI 3100 automatic sequencer. The obtained sequences were submitted to analysis using the Geneious 5.6.5® program. Data were submitted to analysis of variance and to the Tukey-Kramer test at 5% probability and cluster analyses by main components were performed. Allele frequencies were 98 and 97% for the A2 allele and 0.96 and 0.93% for the genotype A2A2 for Gir and Guzerá, respectively. Gir and Guzerá animals showed differences in protein, lactose, and non-fat dry extract levels. Although correlations between milk yield and the production and some milk components are moderate, increases in milk yield are always greater than the increase in constituent yield. In addition, even though Guzerá animals have a higher percentage of protein, lactose, and non-fat dry extract, milk from Zebu breeds is an alternative for individuals sensitive to β-casein protein.