The family Lophoproctidae Silvestri, 1897 includes small, blind millipedes adapted to endogeous environments. The genus Lophoproctus has five species with a mostly Mediterranean distribution, with only one species extending eastwards to Central Asia. Lophoproctus lucidus extends from southern France to north-western Africa and was recently reported for the first time from the Iberian Peninsula and the Canary Islands. However, some populations showed a certain degree of morphological differentiation, suggesting the existence of more than one species. To test this hypothesis, we study Iberian and Canarian populations using scanning electron microscopy and analyse mitochondrial and nuclear sequences of several Lophoproctus species, generating the first phylogenetic hypothesis for the genus. Our results confirm the existence of an unnamed species that is here formally described and named as Lophoproctus viator sp. n. The new species can be differentiated morphologically from the other species of the genus and represents an independent evolutionary lineage. We include a key to the morphological identification of Lophoproctus species.