Amorphophallus yuloensis is a species endemic to southwestern China. Due to the isolated nature of its karst limestone habitat, this species is found in small and isolated populations. Because wild populations of A. yuloensis are in decline due to human activity, it is necessary to assess genetic diversity among A. yuloensis. A total of 96 single nucleotide polymorphism markers were developed and validated for the first time for this species using restriction site-associated DNA sequencing. The average number of effective alleles among these loci was 1.417. The indices of observed and expected heterozygosities ranged from 0.031 to 0.621 and from 0.062 to 0.500, respectively. Nine loci were identified as departing from Hardy–Weinberg equilibrium after Bonferroni correction. These newly developed SNP loci will aid in population genetics research and the conservation of this species in the future.