Armeniaca sibirica L. (Rosaceae) was once an economically important species in China, but the amount of natural germplasm of A. sibirica recently declined dramatically as a consequence of habitat fragmentation and overharvesting; this species has now been listed as endangered in the China Plant Red Data Book. In this study, 72 polymorphic single nucleotide polymorphism (SNP) markers were developed in A. sibirica based on its transcriptome and characterized by genotyping 70 individuals using the SNaPshot method. The minor allele frequency varied from 0.102 to 0.516, and the observed heterozygosity, expected heterozygosity, and polymorphism information content ranged from 0.052 to 0.649, 0.186 to 0.617, and 0.105 to 0.452, respectively. Among these SNPs, seven loci deviated significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (p < 0.05). These novel SNPs can be useful for future population and conservation genetics studies on this species.