Mantisia spathulata Schult. and M. wengeri Fischer, two critically-endangered, endemic and rare species of the genus Mantisia (Zingiberaceae), have been rediscovered from Lunglei province of Mizoram, India, after two decades. For sustainable conservation and utilization of the Mantisia species, in vitro seed and clonal propagation methods have been developed earlier by our research group and plantlets have been reintroduced to their natural habitat for species recovery. To comprehend the plausible reasons for endemism and endangeredness of both the species at DNA level, they were analyzed to assess natural genetic variation using three different polymerase chain reaction (PCR) based DNA markers viz. random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and directed amplification of minisatellite DNA regions (DAMD), both individually and cumulatively, which are popularly regarded as single primer amplification reaction (SPAR) methods. A total of 107 primers belonging to three SPARs are used which collectively endow low genetic variation (15 and 20 %, respectively) in both M. spathulata and M. wengeri. The use and efficacy of SPAR methods to reveal the natural genetic variation in Mantisia species at intra-specific level has been recorded for the first time. To impede the extinction risk of these two species of genus Mantisia, large scale conservation strategies including in situ and ex situ conservation are recommended.