Among direct-developing rain frogs of the genus Craugastor is a clade of 19 described species (bocourti series) that occur in Mexico and northern Central America. Many of these 19 species have been described based on subtle morphological differences and have never been examined using molecular data. Here, we used a multilocus dataset (one mitochondrial (mtDNA) and four nuclear (nDNA) gene fragments, totalling 3,048 concatenated base pairs) to investigate species limits and phylogenetic relationships among 60 northern rain frogs referable to 12 species, with a focus on species from Guatemala. We inferred phylogenies using maximum likelihood and Bayesian analyses on separate mtDNA and nDNA datasets. Concatenated and coalescent species-tree analyses support the monophyly of multiple species, with interspecific relationships mostly unresolved. These mtDNA and nDNA trees were often incongruent with morphology-based taxonomy. For example, two genetically shallow clades contained individuals referable to at least five described species, whereas a single described species contained deep divergences indicative of multiple cryptic species. These findings indicate that morphology-based taxonomy has both overestimated and underestimated actual species diversity (depending on the species), an interpretation supported by two molecular species-delimitation procedures. Based on these findings, we synonymise C. glaucus (Lynch, 1967) and C. stuarti (Lynch, 1967) with C. xucanebi (Stuart, 1941). We also synonymise C. nefrens (Smith, 2005) and C. cyanochthebius McCranie & Smith, 2006 with C. campbelli (Smith, 2005). The molecular data also support multiple undescribed species, notably within C. decoratus (Taylor, 1942). Overall, we show how morphology-based species delimitation can both underestimate and overestimate species richness in morphologically conservative groups.