Cultivation of Capsicum spp. requires a prior growth phase in the greenhouse, and the interaction with arbuscular mycorrhizal fungi (AMF) during this phase can improve such growth. Under greenhouse conditions, this study estimated the effect of colonization by three native AMF (Funneliformis geosporum, Claroideoglomus claroideum, and Glomus ambisporum) during the initial growth of two species of Capsicum (C. chinense Jacq. and C. annuum L.). The results show a high percentage of AMF colonization in the roots of C. annuum (95.98±2.57) and C. chinense (89.75±11.62), with no significant differences among the AMF species (F=0.12, p≤ 0.7308). However, significant differences were present in the Capsicum species in terms of height (F=112.21, p≤0.0001) and fresh root biomass (F= 27.17, p≤0.0001). In all the growth variables, an interaction between the AMF and Capsicum species was observed (F≥12.43, p<0.05), suggesting differential effects of the AMF species. In the interaction of C. claroideum and C. annuum, the seedlings presented significantly greater height, dry aerial biomass, fresh and dry root biomass, while G. ambisporum triggered greater height and root biomass in C. chinense seedlings. Our results show that inoculation with native AMF can increase the initial performance of Capsicum species. keywords Interaction, Funneliformis geosporum, Claroideoglomus claroideum, Glomus ambisporum, sweet chili, habanero chili resumen El cultivo de Capsicum spp. requiere una fase de crecimiento en invernadero, la interacción con hongos micorrizógenos arbusculares (HMA) durante esta fase puede incrementar este crecimiento. En este estudio se estimó, bajo condiciones de invernadero, el efecto de la colonización por tres especies nativas de HMA (Funneliformis geosporum, Claroideoglomus claroideum y Glomus ambisporum) en el crecimiento temprano de dos especies de Capsicum (C. chinense Jacq. y C. annuum L.). Los resultados muestran un alto porcentaje de colonización micorrízica en las raíces de C. annuum (95.98±2.57) y C. chinense (89.75±11.62), sin diferencias significativas entre especies de HMA (F=0.12, p≤ 0.7308). Sin embargo, se presentaron diferencias significativas entre las especies de Capsicum en altura, (F=112.21, p≤0.0001) y biomasa fresca radical (F= 27.17, p≤0.0001). En todas