The Craugastor mexicanus series (Anura: Craugastoridae) includes six species of direct-developing frogs that occur in Mexico and Guatemala. Notably, two of these species have small adult body sizes (<18 mm snout to vent length) and several have intraspecific polymorphism in color pattern. Using a geographic sampling focused on eastern Mexico (the location of most type localities), we conducted a molecular phylogenetic analysis of two mitochondrial (12S, 16S) and two nuclear (RAG1, TYR) gene fragments. This analysis revealed two widespread species, C. mexicanus and C. pygmaeus, along with evidence of multiple undescribed taxa from the states of Oaxaca, Mexico, Guerrero, and Jalisco. Interestingly, the widespread species have stratified geographic distributions with the larger bodied clade restricted to high elevations and the smaller bodied clade to low elevations. We also identify regions of Guerrero and Oaxaca where multiple species co-occur. To reevaluate the quality of characters that have been previously used to diagnose species, we tested for heterochrony and sexual dimorphism using microcomputed tomography and linear measurements. We found evidence for paedomorphosis as the mechanism of miniaturization in small-bodied taxa. Linear measurements confirmed that tympanum and body size are sexually dimorphic traits in both small- and large-bodied species. We used this enhanced understanding of morphological variation in the group to describe six new species. Despite this progress, we suspect that additional species await discovery, particularly in western Mexico and east of the Isthmus of Tehuantepec where our sampling efforts were limited.