The genus Capsicum is an economically important plant around the world. In Mexico, chili cropping is a profitable agricultural business due to its demand in the national and international market. A species of interest is the piquín chili pepper, Capsicum annuum var. glabriusculum (Dunal) Heiser & Pickersgill, whose exploitation is limited only to wild populations. There have been many unsuccessful attempts to cultivate it intensively because of its low germination percentage, since the seed shows non-deep physiological dormancy, a frequent feature in undomesticated wild species. In this study, the effect of temperature and times of storage of piquín chili pepper seed on the concentration of tryptophan (auxin precursor amino acid), cytokinins (kinetin) and gibberellins (GA3) and their germinative capacity were analyzed. For this, the germinative capacity of pepper seeds stored at two temperatures (4 and 24 °C) and five times (0, 3, 6, 9 and 12 months) was evaluated. Also, quantification of the phytohormones auxins, cytokinins and gibberellins was performed using high performance liquid chromatography (HPLC). The results show that the content of the three phytohormones had increased through time according to the time of storage. The highest germination percentage was at 9 months of storage and this was the highest content of the three phytohormones; however, at 12 months of storage, germination started diminishing as well as the phytohormone content, indicating that the seed quality and viability was starting to decrease.