Cladonia jaliscana is a lichen forming fungus, common, and abundant mainly in temperate forests of Mexico, which has received little attention in the literature. It is characterized by a conspicuous and persistent primary thallus, clavate podetia, red hymenial disc, and containing didymic and thamnolic acids as major substances. In this study we re-examine C. jaliscana from a morphological, chemical, and phylogenetic perspective. New specimens were collected from Durango, Jalisco, Veracruz, and Zacatecas, Mexico. Additionally, specimens from different herbaria were studied (ENCB, IBUG, MEXU, and XAL) including the holotype and two paratypes. A phylogeny of Erythrocarpae clade was estimated using ITS rDNA, rpb2, and tef1 by Maximum Likelihood analysis and Bayesian inference. Cladonia jaliscana was recovered as monophyletic within Subglaucescentes subclade, in Erythrocarpae clade. Cladonia leprocephala, C. meridensis, and C. microscypha formed a sister clade of C. jaliscana. A new chemotype containing barbatic acid was found in this species. The description of the species was updated to include morphological and chemical variation. The intra-specific genetic variation of C. jaliscana was explored using haplotype networks and FST test. These analyses showed some geographical structure. Genetic differentiation of the Veracruz population was accompanied by morphological and chemical differences, indicating some genetic isolation. Keywords: Ascomycota, Jalisco, Lecaronomycetes, lichen systematics, Mexico.