Staphylococcus equorum is a benign bacterium and the predominant species in high-salt fermented food. Some strains of S. equorum contain antibiotic-resistance plasmids, such as pSELNU1 that contains a lincosamide nucleotidyltransferase (lnuA) gene and confers resistance to lincomycin. Previously, we showed that pSELNU1 is transferred to other bacteria under laboratory growth conditions. However, it is not known if the plasmid can be transferred to other bacteria during food fermentation (in situ) or during passage through animal intestines (in vivo). In this study, we examined the in situ and in vivo transfer of pSELNU1 using Staphylococcus saprophyticus as a recipient. During soybean fermentation, pSELNU1 was transferred to S. saprophyticus at a rate of 1.9 × 10−5–5.6 × 10−6 per recipient in the presence of lincomycin. However, during passage through murine intestines, the plasmid was transferred at similar rates (1.3 × 10−5 per recipient) in the absence of lincomycin, indicating that the plasmid transfer is much more efficient under in vivo conditions. Based on these results, we conclude that it is prudent to examine food fermentation starter candidates for the presence of mobile genetic elements containing antibiotic resistance genes and to select candidates lacking these genes.