Chayote (Sechium edule) is a crop of great economic and pharmaceutical importance in Mexico. Chayote is affected by Phytophthora capsici, which causes plant wilt and fruit rot. Three isolates of P. capsici (A1-C, A2-H, and A3-O) were obtained from three producing areas in Veracruz, Mexico. Morphometric characteristics of sporangia and the colony pattern on three different media were described. They were molecularly identified by amplification of the internal transcribed spacer region (ITS) and the partial sequence of cytochrome c oxidase subunit 1 (COI), sequences that were phylogenetically analyzed. The mating type, pathogenicity in S. edule fruits, and sensitivity to metalaxyl were determined. Isolate A1-C presented the largest sporangium; all sporangia were papillated, with different morphologies and pedicel lengths. All isolates showed different colony patterns: chrysanthemum (A1-C), stellate (A2-H), and petaloid (A3-O). The topology of the phylogenetic tree was similar for the ITS region and COI gene, the sequences of the three isolates clustered with sequences of the genus Phytophthora classified in group 2b, corroborating their identity as P. capsici. The mating type of isolates A1-C and A3-O was A2 and of isolate A2-H was A1. The pathogenicity test indicated that isolate A1-C was the most virulent and with intermediate sensitivity to metalaxyl. This work suggests that P. capsici isolates from various production areas in Mexico may exhibit morphological and virulence variability.