Lactiplantibacillus plantarum, a typical ecological species against pathogens, used due to its bacteriocin yield in fermented foods, was proven to have the capacity to lower cholesterol. In this study, using L. plantarum ATCC8014 as the control, L. plantarum WLPL21 and ZDY04 were probed with whole-genome sequencing to ascertain their potential ability to lower cholesterol and yield bacteriocins, as well as to further evaluate their survival capacity in vitro. Our results showed 386 transport-system genes in both L. plantarum WLPL21 and ZDY04. Correspondingly, the in vitro results showed that L. plantarum WLPL21 and ZDY04 could remove cholesterol at 49.23% and 41.97%, respectively, which is 1.89 and 1.61 times that of L. plantarum ATCC8014. The survival rates of L. plantarum WLPL21 and ZDY04 in 1% H2O2, pH 3.0, and 0.3% bile salt were higher than those of L. plantarum ATCC8014. Our results exhibited a complete gene cluster for bacteriocin production encoded by L. plantarum WLPL21 and ZDY04, including plnJKR, plnPQAB, plnEFI, plnSUVWY, and plnJK; and plnMN, plnPQA and plnEFI, respectively, compared with only plnEF in L. plantarum ATCC8014. The present study suggests that the combination of genomic analysis with in vitro evaluations might be useful for exploring the potential functions of probiotics.