Natural gums are one of the important non-timber forest products (NTFP) in India. India is endowed with highly diverse gum-yielding tree species and is a leading producer of natural gums (Basch et al., 2004). Olibanum, an oleo-gum-resin, is obtained from the bark of Boswellia Roxb. ex Colebr. species (Burseraceae). Boswellia serrata Roxb. ex Colebr. (Leung and Foster, 1996), one of four species in the genus Boswellia, is an endangered species that is found in dry deciduous forests of India, Pakistan, and Arabia (Ghorpade et al., 2010). It is often referred to as Indian frankincense and is locally called dhoopa or salai guggal. Boswellia serrata is a moderate-to large-sized tree found in the deciduous forests of Western Ghats, Eastern Ghats, Rajasthan, Gujarat, Uttar Pradesh, and in other dry and tropical regions of India. Burning B. serrata resin as incense has been part of religious and cultural ceremonies since time immemorial. Boswellia serrata gum-resin contains essential oils, volatile oils, sugars, and terpenes with β-boswellic acid (Siddiqui, 2011). In recent years, B. serrata has attracted the attention of pharmacologists for the development of nonsteroidal anti-inflammatory drugs (NSAIDs) because of its chemical constituents (Singh et al., 1996). Oleo-gum-resin of B. serrata is used in the treatment of ulcerative colitis, Crohn’s disease, osteoarthritis, rheumatoid arthritis, joint pain (rheumatism), bursitis, abdominal pain, asthma, hay fever, sore throat, syphilis, and liver disorders; it can act as an anti-inflammatory agent by inhibiting the synthesis of 5-lipoxygenase (Siddiqui, 2011). Boswellia serrata extract also exhibits antibacterial, antifungal, and antimicrobial activities (Ismail et al., 2014). In recent years, it has also been used in cosmetics and perfumes. In India, approximately 1500 tons of B. serrata gum is harvested annually (Giri et al., 2008). With increasing demand for resin, unsustainable harvesting practices, anthropogenic threats, and lack of regeneration (Tandon et al., 2010) have resulted in the rapid decline of populations of the species. Extraction of the resin by puncturing or damaging the bark can cause trees to be susceptible to pests or diseases, and indiscriminate extraction could lead to mortality. This adult mortality, in combination with fragmentation and low regeneration, threatens the persistence of the species. Boswellia serrata is now reported as a rare species in the Red Data Book of India (Modi and Mathad, 2016). Despite its economic importance, knowledge of the genetic resources of this species is scarce. Information on the genetic diversity and pattern of genetic differentiation across populations is crucial for designing appropriate conservation strategies. Addisalem et al. (2015) developed microsatellite markers for B. papyrifera. However, when we used these markers in B. serrata, we found their amplification efficiency to be low. In this study, we developed microsatellite markers for B. serrata with high efficiency and tested their applicability in the related species B. ovalifoliolata N. P. Balakr. & A. N. Henry.