Notopterygium oviforme (Apiaceae) is an endangered perennial herb endemic to China. To investigate its population genetics, we characterized 17 novel microsatellite markers based on high throughput Illumina MiSeq sequencing data. The number of observed alleles (N_O) per locus varied between 1 and 7 (mean = 3.53). Observed and expected heterozygosities (H_O and H_E, respectively) ranged from 0.24 to 0.72, and from 0.37 to 0.64, respectively. Fourteen primers were successfully cross-amplified in two congeneric species (N. incisum and N. forbesii). We detected no deviation from the Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) at any loci. These microsatellite markers are likely to be useful for the study of population genetic diversity and genetic structure of N. oviforme and its congenerics.