Selenicereus megalanthus is a native fruit tree with broad phenotypic variations that has not been characterized. The objective of this research was to morphoagronomically evaluate yellow pitahaya genotypes in open fields and under cover in the municipality of Miraflores, Boyacá. A diagnostic census of the productive system was carried out. The morphoagronomic characterization used a completely random design with qualitative and quantitative descriptors for fruits and cladodes taken in situ and analyzed with frequency, descriptive, multivariate, conglomerate, and sperm correlation analyses. The pitahaya production system was based on empirical practices carried out by farmers. The weight of the largest fruit in open fields was 219.04 g on average; the average was 186.48 g with the covered system. The open-field systems had the largest genotypes in all the dimensions (length and width). The covered systems had the highest number of fruits per cladode (3.70) and the longest cladodes in the entire study (121.24 cm). Both production systems showed similar values for titratable acidity (0.20), and the soluble solids values were slightly higher in the open-field system than in the covered system (15.20 and 14.66 °Brix, respectively), desirable characteristics for the market. Genotypes 7 (under cover) and 3 (open field) presented outstanding morphological and agronomic characteristics. This study identified genotypes that can be included in selection programs for yellow pitahaya in Miraflores, Colombia.