Among the settlers that, from 1432 onwards, arrived to the Azores Islands were individuals of North and sub-Saharan African origin. A previous study of markers of the Y chromosome revealed that haplogroup E is the second more frequent in the Azores (13%). Since this haplogroup is heterogeneous and may contain subtypes of African or non-African origin, we analyzed an extended sample of 319 Azoreans, originating from the three groups of islands (Eastern, Central, and Western), to evaluate the African contribution to the present-day population of the Azores. Samples belonging to the E clade were distributed into six haplogroups, from which the most frequent was E3b1a, representing 47.2% of the E chromosomes (6.3% of the total sample). The sub-Saharan haplogroup E3a was found in 7.1% of E chromosomes (0.9% of the total), corresponding to the highest frequency reported so far in a Portuguese population. No significant differences were detected in the haplogroup distribution among groups of islands, as well as between Azores and most of other European populations compared. The present-day representation of sub-Saharan lineages in Azores, although reduced, is higher than in other Portuguese populations, where the demographic representation of sub-Saharan slaves is reported as similar.