Multidrug-resistant (MDR) bacteria in farm animal products threaten human health by causing zoonotic infections. The complete genome sequences of MDR bacteria from subclinical mastitis-affected cow's milk have not yet been comprehensively documented in India. In this study, using a bacterial metagenomic sequencing approach, we detected the nearly complete genome sequences of and s from subclinical mastitis-affected cow's milk. Furthermore, we sequenced the nearly complete genome sequences of , , , and from subclinical mastitis-affected cow's milk using a whole-genome metagenomic sequencing method. Our analysis subsequently revealed that the complete genome sequences of the identified bacteria contained MDR genes and genes for multiple virulence factors. These MDR bacteria may pose a public health risk through exposure to milkers, milk handlers, and farm workers or through the handling and consumption of unpasteurized milk.