Micropropagation of Psidium guajava L. (guava) is a viable alternative to currently adopted techniques for large-scale plant propagation of commercial cultivars. Assessment of clonal fidelity in micropropagated plants is the first step towards ensuring genetic uniformity in mass production of planting material. In the present study, 31 plants of guava cultivar “Lucknow 49” regenerated by micropropagation were tested for genetic fidelity by comparing them to the mother plant from which explant material was obtained. Efficient rooting of in vitro proliferated shoots was obtained by culture on 1/2 strength MS medium supplemented with either 9.8 μM indole butyric acid (IBA) or 11.4 μM indole acetic acid (IAA). Leaf samples of 31 regenerated plants were compared to the mother plant using 17 simple sequence repeat (SSR) markers. While 16 SSRs detected the same allele, locus mPgCIR07 detected slight differences, where six micropropagated plants were 1 bp smaller (152 bp) than the parental genotype (153 bp). Differences in leaf tissues for anthocyanin pigmentation were also noted among micropropagated plants. Results of the study indicated efficient rooting of “Lucknow-49” cultivar for rapid propagation of planting material, and revealed that micropropagated plants were identical for 16 of the 17 loci examined. Although most mutations induced by tissue culture may not have an effect on phenotype, the possibility that novel phenotypes can be generated in a commercial setting exists.