Guazuma crinita is an important fast-growing timber tree species widely used in agroforestry systems in the Peruvian Amazon. The objectives of our research were (i) to assess genetic diversity of G. crinita using inter-simple sequence repeat (ISSR) markers and (ii) estimate correlation between genetic and geographic distances among provenances. The sample included 44 genotypes from 11 provenances in the Aguaytia and neighboring Pachitea watersheds in the Peruvian Amazon. Ten ISSR primers amplified a total of 65 bands of which 61 were polymorphic (93.8%). The range of DNA amplification varied from 260 to 2,200 bp. Among the provenances, Macuya exhibited the highest percentage of polymorphic bands (PPB) with 67.7%, 0.21 Nei’s gene diversity (He) and 0.33 Shannon index (I). Overall genetic differentiation (Gst) was 0.03, indicating 97% of genetic diversity within provenances. Gene flow (Nm) was 12.9 alleles per generation. Cluster analysis was not related to geographic origin, suggesting a common gene pool. However a weak positive correlation (r = 0.27, P < 0.05) was found between genetic and geographic distance. This is the first study of genetic diversity and structure of G. crinita. We recommend in situ conservation strategies for populations with high levels of genetic diversity. © 2016, Universidad Austral de Chile. All rights reserved.