Lactobacilli are predominant bacterial species colonizing the vaginal surfaces of healthy women, where they play a protective role against opportunistic and polymicrobial infections such as Bacterial Vaginosis (BV). Several Lactobacillus species, especially L. crispatus, have been prospected for probiotic applications due to their potential antimicrobial and anti-inflammatory capacity. In the last decade, several genomic studies have investigated the genetic factors of L. crispatus strains for identifying novel probiotic strains and evaluating their application for improving human or animal health. This mini-review highlights the primary genes associated with L. crispatus protective mechanisms identified, in our previous work, on four novel strains isolated from healthy Brazilian women of reproductive age. Among the probiotic features discussed, the role of a pyruvate oxidase-encoding gene, lactate synthesis-related enzymes, bacteriocins genes, and genomic islands is reviewed, and the following steps to confirm their activity are pointed out.