Rhododendron longipedicellatum is an endangered species endemic to southeastern Yunnan, China. Assessment of genetic variation is critical for protecting endangered species. Therefore, we used EST-SSR markers to analyze the genetic characteristics of R. longipedicellatum. The results revealed high genetic diversity at the species level ( He = 0.559, NA = 9.529) and within populations ( He = 0.507, NA = 5.910) and moderate genetic differentiation between populations ( FST = 0.083). In addition, more genetic variation existed within populations (91.25%) compared with variation among populations (8.75%). The STRUCTURE analysis showed that 150 individuals from five existing populations could best be divided into two genetic groups. At the population level, the neighbor-joining (NJ) tree and principal coordinates analysis (PCoA) analyses also divided them into two groups. In addition, Bottleneck analyses using the Two-Phase Model (TPM) and Stepwise Mutation Model (SMM) as well as the Garza-Williamson Index revealed widespread signatures of bottleneck events. These results provide vital information for scientifically formulating conservation strategies for the endangered R. longipedicellatum.