It has been suggested in the literature that limited hybridization occurs between Cupressus macnabiana and C. sargentii where the species occur in sympatry. This study confirmed the hybrid origin of specimens from a sympatric population using an objective analysis of morphological and DNA evidence. Fifty–eight individuals from three populations (two pure stands and one mixed population) were sampled. Variation in diagnostic restriction sites within ITS (nrDNA), matK (cpDNA), and NEEDLY intron two (nDNA) were used in combination with 20 quantitative morphological characters to detect and characterize putative hybrids. ITS and NEEDLY were uninformative with respect to hybrid detection, but matK demonstrated species–specific polymorphism. Anomalous combinations of plastid type, Discriminant Function identification, and position in a pictorialized scatter diagram were used to identify putative hybrids. Intermediacy of the putative hybrids was demonstrated statistically (p = 0.005) with 13 out of the 14 diagnostic morphological characters having intermediate values. Hybrids most likely arose from multiple hybridization events with both species acting as the paternal parent. The hybrids are apparently fertile, and may form a complex swarm. The most recognizable morphological characteristics of the hybrids are the partial development of resin glands on leaves of the ultimate branch segments, the penultimate branching pattern, ovulate cone width, and seed mass.