Sweet pepper (Capsicum annuum L.) is considered as the most important vegetable crop worldwide. Association mapping based on linkage disequilibrium is a capable tool to identify genes controlling plant agrobiological characteristics. In this study, an association panel consisting of 29 indigenous sweet pepper accessions were collected from several geographical regions of Iran. The panel was evaluated phenotypically for sixteen fruit as well as plant architecture traits across two locations under field conditions. In molecular experiment, 10 inter simple sequence repeat (ISSR) markers were used for genomic fingerprinting of accessions. Results revealed abundant phenotypic variations within this germplasm and a total of 65 markers ranging from 3 to 10 per primer were identified in all accessions. Model-based structure analysis revealed two subpopulations. Out of 29 native sweet pepper accessions studied, 93.1% belonged to one of the two identified subpopulations and 6.9% showed mixed structure. A total of 17 marker-trait associations were detected based on a mixed linear model, of which one (UBC825-1) was found as a common marker for some agrobiological characters. The favourable 17 marker loci can be utilized in plant architecture breeding programmes according to specific breeding objectives.