Introduction: Lipoprotein L21 (LipL21) has been used as a molecular marker for leptospirosis as it is highly expressed in pathogenic Leptospira species during infection. However, it lacks specificity due to the newly emerging pathogenic serovars. Therefore, interrogation of LipL21 in all serovars needed to understand the pathogenesis of leptospirosis to enable early diagnosis. This study was carried out to determine the suitability of LipL21 as a molecular marker for leptospirosis by identifying the conserved sequences of LipL21 mRNA and amino acids in different Leptospira strains. Methods: Location of LipL21 conserved regions in 15 pathogenic and 2 non-pathogenic strains of five Leptospira species, were identified using bioinformatics database and tools such as National Center of Biotechnology, Rapid Annotation Subsystem Technology blast search, Muscle program and Jalview software. Results: Multiple sequence alignment analysis revealed that two conserved regions were observed in 10 pathogenic Leptospira strains from nucleotide position 29 to 53 and 100 to 137, however conserved amino acid sequences (111-149 and 155-192) were found in all the pathogenic strains. The distinction between gene and amino acid results is due to the degenerate genetic code feature. Conclusion: In conclusion, this study suggests that LipL21 protein has a potential to be used as a diagnostic marker for detection of Leptospira pathogens compared to LipL21 mRNA.