Lactobacillus (LAB) genera are considered important functional food but are found to have a short shelf life. In this study, two LAB, Lactobacillus plantarum (Lp) and Lactobacillus rhamnosus (Lr), were isolated from sheep’s milk, and whole-genome sequencing was carried out by using 16s rRNA Illumina Nextseq, the Netherlands. The LAB were encapsulated by the lyophilisation technique using different lyoprotective pharmaceutical excipients. This process was carried out using a freeze dryer (U-TECH, Star Scientific Instruments, India). Shelf-life determination was carried out by a 12-month study using the viability survival factor (Vsf). The in vitro cell adhesion technique was carried out by using the red snapper fish along with autoaggregation and cell surface hydrophobicity as vital probiotic properties. It was observed that Lp has a significantly higher (P < 0.001) Vsf of 7.2, while Lr has a Vsf of 7 (P < 0.05) when both are encapsulated with 10% maltodextrin + 5% sucrose kept at 4°C for 12 months. The result demonstrated that Lp had significantly high (P < 0.05) cell adhesion, 96% ± 1.2 autoaggregation, and 6% cell surface hydrophobicity as compared to Lr. Moreover, this study demonstrated that lyophilised LAB with lyoprotective excipients enhances shelf life without any changes in probiotic properties when kept at 4°C exhibiting all its probiotic properties.