The diversity of the tropical climbing salamander genus Bolitoglossa (Magnadigita) in Honduras has been underestimated historically, with 11 new species having been described in the past quarter-century. Bolitoglossa celaque is known to occur in three disjunct mountain ranges across the Lenca Highlands region of southwestern Honduras, and previous studies have independently demonstrated differences in mitochondrial genealogy and genome size between populations to the east and west of the Mejocote–San Juan Depression. Sampling from all three mountain ranges represented two genetically distinct clades: one associated with the vicinity of the type locality, Montaña de Celaque, and the second consisting of several eastern populations from the departments of Intibucá and La Paz. Distinctiveness of these two clades was further investigated and supported by analyses of morphological variation, geometric morphometrics of foot morphology, and comparative osteology. Based on congruent signals from each line of evidence, we restrict the taxon B. celaque to Montaña de Celaque and describe the eastern populations as a new species of Bolitoglossa.