Polymorphic microsatellite markers were developed in Annona deceptrix (Annonaceae) to evaluate its genetic diversity and population structure. This species is a relevant agricultural and food resource for society because its edible fruit that can be considered as a consumption option. However, natural populations have a high degree of vulnerability caused for human activities and disturbances. The objective of this study was to isolate and characterize SSR loci as a tool to determine the genetic diversity in A. deceptrix and others in Annonaceae family. Twenty-two polymorphic Simple Sequence Repeat (SSR) loci were isolated from A. deceptrix using a new-generation kit Nextera of miseq illumine technology. The mean number of alleles per locus ranged from 2 to 8. Observed and expected heterozygosity ranged from 0.00 to 1.0 and 0.00 to 0.93, respectively. The average the inbreeding coefficient in the Humedad site was 0.007, while in Agua Blanca and Tachina, they obtained negative values of -0.090 and -3.222, respectively. These are the first microsatellite markers developed for A. deceptrix. All SSR markers developed are promising candidates for analysing genetic variation within or between natural populations and can be transferable to other species of the genus Annona.