Abstract Aim We analyse the influence of different factors on the inter-insular colonization processes that yielded the current distribution pattern of endemic reptile species in the Canary Islands. Location The seven main islands of the Canary Islands. Methods We tested 11 hypotheses about factors that might have affected the colonization processes. We used Mantel and partial Mantel tests to establish the statistical significance of the relationship between the islands predicted by each hypothesis, and a parsimony analysis to detect the most parsimonious hypothesis. Results The only significant relationships were those predicted by inter-island distance, also taking area into account, and habitat similarity, considering current vegetation in the islands. The latter was the best hypothesis according to the parsimony criterion. Main conclusions Our results support the hypothesis that habitat similarity between islands is the main factor affecting the colonization processes of the whole group, although inter-insular distance seems to play a separate role in colonization events.