<p><strong>Background.</strong> Mexico has a great diversity of chili peppers, especially in <em>C. annuum</em> L., which includes local morphotypes that have been little studied. Apaxtleco chili pepper is only found in Guerrero State, Mexico, and it is important in Apaxtla region due to economic resources it generates, and because it is used in preparation of typical mole in this region; however, its morphological diversity has not been described and this visualizes the state of this plant genetic resource to define use and conservation strategies. <strong>Objective. </strong>To analyze and describe morphological diversity of a group of Apaxtleco chili pepper populations, identify characteristics that most support its diversity and establish similarity relationship between the populations studied. <strong>Methodology. </strong>Twenty-four populations of apaxtleco chili pepper collected from Apaxtla de Castrejón, Guerrero were evaluated under randomized complete block experimental design, with four replications. The evaluation was carried out under greenhouse conditions at Tuxpan Unit of Autonomous University of Guerrero. Sowing was carried out in July 2020 in polyethylene pots with 16 L capacity. Fifty-nine morphological variables from IPGRI descriptors for <em>Capsicum</em> were recorded, and variance, discriminant, principal components (CP) and conglomerated analysis were performed by SAS V9.3 software. <strong>Results. </strong>Statistical significant differences were found in 72.9 % of variables registered and seventeen were selected by its contribution to variation according discriminant analysis, which were mostly fruits characteristics. In CP, with the first six, 76 % of total morphological variation was explained; length fruit and pedicel, width seed, weight fruit per plant, color of fruit at intermediate stage, number fruits per plant, width fruit, fruit and seed texture, filament color, number seeds per fruit and shape fruit appendage had greater contribution to total morphological diversity and were useful to differentiate populations under study. As well, four groups of apaxtleco chili pepper with different fruit, vegetative and flower characteristics were identified, however, it was possible to group them by shape and texture of fruits. <strong>Implications.</strong> Contribute to description of diversity of local populations of apaxtleco chili, native to Guerrero, Mexico, and that allows the establishment of use and conservation mechanisms for food security. <strong>Conclusion.</strong> Morphological diversity of native apaxtleco chili of Guerrero is presented mainly in fruit characteristics and lesser degree in vegetative and seed traits, which were useful to explain greater total variation in this local chili. The shape and texture fruits were important characteristics in grouping.</p>