The conservation status of an ecosystem is checked by studying the composition and diversity of the organisms that interact in trophic chains. The aim of this study was to evaluate the biodiversity of mites associated to Capsicum annuum L. var glabriusculum (Solanaceae) at three sampling sites corresponding to two Protected Natural Areas (PNA) in Tamaulipas state, Mexico. Samplings were carried out in “Cañón de la Peregrina” and “Altas Cumbres” situated in the PNA “Altas Cumbres” and “Ojo de Agua”, located in the “El Cielo” Biosphere Reserve. Mite diversity was H = 1.09 ± 0.14 in Ojo de Agua, and it was H = 1.08 ± 0.08 and H = 1.11 ± 0.06 in Altas Cumbres and Cañón de la Peregrina, respectively. A total of 47 species were identified belonging to 35 genera of 18 families associated to C. annuum L. var glabriusculum in Mexico. Predatory mite richness was higher than that of generalist and phytophagous mites (31, 11 and 5 species, respectively) for the two ANP. The similarity index of Jaccard between OA–AC (I_J = 0.257; P < 0.05), CP–AC (I_J = 0.293; P < 0.05) and AC–CP (I_J = 0.324; P < 0.05) was low. Pseudopronematalus sp. 4 (Iolinidae) was predatory mite most abundant in both ANP (P_i = 9.311); followed by Metaseiulus (Metaseiulus) negundinis (Denmark) (Phytoseiidae) only for ANP “Altas Cumbres” (P_i = 1.004). While for phytophagus mite, Aculops lycopersici (Tryon) (Eriophyidae) and Tetranychus merganser Boudreaux (Tetranychidae) presented the highest abundances in all sites (P_i = 79.919 and 5.142, respectively). The high number of mites species associated to chile piquín suggests stability in the PNA despite anthropogenic activities, and that the PNA works as a mite reservoir.