The evolutionary relationships of amphisbaenians of the genus Blanus have long been controversial. Presently two species are recognized for Morocco — Blanus tingitanus and B. mettetali and one for Iberia — B. cinereus. Using mitochondrial and nuclear DNA sequences, 25 samples from Portugal, Spain and Morocco were analysed. Both markers indicate the existence of three well-separated clades: one for the Northern Moroccan samples, corresponding to B. tingitanus and two to the B. cinereus samples. One sample from Taza, Morocco, was identical to specimens from one of the Iberian forms. These results point to the necessity of a systematic revision. These new groups reinforce the need for geographically broader sampling accompanied by morphological studies to fully determine the phylogenetic history of this species complex.