We analyzed size variation of Hemileia vastatrix coffee leaf rust urediniospores. Further, the morphological structure and vegetative hyphae of uredinia were examined. The study included isolates collected in 17 coffee cultivars grown at various altitudes (229 to 1,649 m) in 14 regions of four Mexican states. In 2015, 265 leaf samples with rust symptoms were collected from Coffea arabica, Coffea canephora, and Catimores (C. arabica × Timor hybrid) trees (n = 3,808 leaves). Thirty spores per sample, on a final subset of 65 leaves (n = 1,950 spores), were measured and grouped using the Ward centroid method. Uredinia morphology and vegetative hyphae in lesions and tissue sections were examined by electron microscopy. Pathogen identity was confirmed based on symptoms, morphology, and ITS-rRNA sequence analysis. We identified eight significant groups of spores based on size. Groups 8h and 3a had a smallest and largest spore size respectively, and groups 1b–7f having a variable intermediate size. Novel structures were observed on uredinia: double-cell walls on pedicel and urediniospores, split septum between spore and attached pedicel, apical half-septum wall covering the pedicel, and urediniospore ventral side protuberances and hilum; and on lesions: leaf surface and intracellular hyphae anastomoses, and haustoria anastomoses. It is suggested that urediniospore size variation may facilitate interaction to the diversity of coffee cultivars and environmental conditions, and doble cell wall involved for spore development, release, and protection; and anastomoses are likely sources of H. vastatrix acquire nonsexual variation. These findings encourage further analysis for management coffee rust disease.