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The emergence of antimicrobial-resistant and mastitis-associated Staphylococcus aureus is of great concern due to the huge economic losses worldwide. Here, we report draft genome sequences of two Staphylococcus aureus strains which were isolated from raw milk samples obtained from mastitis-infected cows in Bangladesh. The strains were isolated and identified using conventional microbiological and molecular polymerase chain reaction (PCR) methods. Antibiotic susceptibility testing was performed. Genomic DNA of the two strains was extracted and the strains were sequenced using the Illumina NextSeq 550 platform. The assembled contigs were analyzed for virulence determinants, antimicrobial resistance genes, extra-chromosomal plasmids, and multi-locus sequence type (MLST). The genomes of the two strains were compared with other publicly available genome sequences of Staphylococcus aureus strains. The raw read sequences were downloaded and all sequence files were analyzed identically to generate core genome phylogenetic trees. The genome of BR-MHR281strain did not harbour any antibiotic resistance determinants, however BR-MHR220 strain harbored mecA and blaZ genes. Analysis of BR-MHR220 strain revealed that it was assigned to sequence type (ST-6), clonal complex (CC) 5 and spa type t304, while BR-MHR281 strain belonged to ST-2454, CC8, and harbored the spa type t7867. The findings of the present study and the genome sequences of BR-MHR220 and BR-MHR281 strains will provide data on the detection and genomic analysis and characterization of mastitis-associated Staphylococcus aureus in Bangladesh. In addition, the findings of the present study will serve as reference genomes for future molecular epidemiological studies and will provide significant data which help understand the prevalence, pathogenesis and antimicrobial resistance of mastitis-associated Staphylococcus aureus ., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)