The data are supplementary materials for the research article "First DNA sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants". The aim of the study was to investigate polymorphisms in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB, and casein haplotypes in Beninese indigenous cattle. For this ... purpose, the exon sequences, flanking intron sequences and parts of the 5’-upstream regions of milk protein genes were sequenced in 67 Beninese indigenous cattle. Further details in the methodology and the main findings are provided in the article. The supplementary data include five tables: Table S1. Primer sequences utilized for the sequencing of the six milk protein genes (CSN1S1, CSN2, CSN1S2, CSN3, LALBA, LGB) in the Beninese indigenous cattle breeds; Table S2. List of the bovine miRNA and their corresponding seed sequences retrieved from the TargetScan website and used in “targetscan_60.pl” tool for the detection of miRNA target sites; Table S3. List of the polymorphisms detected within the exon sequences, flanking intron sequences and parts of the 5’-upstream regions of milk protein genes (CSN1S1, CSN2, CSN1S2, CSN3, LALBA, LGB) in Beninese indigenous cattle breeds; Table S4. Distributions of variant types (according to their positions and consequence) de-tected within each of the six milk protein genes (CSN1S1, CSN2, CSN1S2, CSN3, LALBA, LGB) and total in Beninese indigenous cattle breeds; Table S5. Functional consequence of the frameshift insertion of nucleotide A at BTA11:103257980 on the translational reading frame and on mature protein.