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A novel coagulase-negative <i>Staphylococcus</i> strain (H164^T) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164^T strain is a member of the genus <i>Staphylococcus</i>. We used multilocus sequence analysis (MLSA) and phylogenomic analyses to demonstrate that the novel strain was closely related to <i>Staphylococcus gallinarum</i>, <i>Staphylococcus nepalensis</i>, <i>Staphylococcus cohnii</i>, and <i>Staphylococcus urealyuticus</i>. The average nucleotide identity and digital DNA-DNA hybridization values between H164^T and its closest relatives were <95% and <70%, respectively. The H164^T strain could also be distinguished from its closest relatives by the fermentation of _{<span style="font-variant: small-caps;">d</span>}-fructose, _{<span style="font-variant: small-caps;">d</span>}-maltose, _{<span style="font-variant: small-caps;">d</span>}-trehalose, and _{<span style="font-variant: small-caps;">d</span>}-mannitol, as well as by the activities of α-glucosidase and alkaline phosphatase. The major cellular fatty acids were C15:0 iso and C15:0 anteiso, and the predominant menaquinones were MK-7 and MK-8, respectively. The major cellular fatty acids and predominant menaquinones were C_15:0 iso and C_15:0 anteiso and MK-7 and MK-8, respectively. In conclusion, this strain represents a novel species, named <i>Staphylococcus hsinchuensis</i> sp. nov., with the type strain H164^T (=BCRC 81404^T = NBRC 116174^T).