The pear‐cypress rust Gymnosporangium asiaticum is one of the most significant causal agents of pear rust in Asian pear, severely affecting the pear industry. Research on the genetic diversity of this widespread pathogen has been hampered due to the absence of molecular markers. In the current study, we developed 16 novel microsatellite markers for G. asiaticum from transcriptome data by combining next‐generation sequencing and PCR screening. These polymorphic markers were tested on 96 individuals from nine provinces in China. The number of alleles for these markers ranged from two to nine, with an average of five at each locus. The polymorphic information content ranged from 0.0411 to 0.7666, with an average of 0.4417. In addition, the observed (HO) and expected (HE) heterozygosities were 0.0312–0.6941 and 0.0417–0.8000, respectively. We also observed low‐to‐moderate levels of genetic differentiation and extremely significant gene flow between the nine provinces. Of these 16 developed simple sequence repeat loci, 11 were transferable to other Gymnosporangium species. These new microsatellite markers can be used in future large‐scale studies of the genetic structure and diversity of G. asiaticum.