This study provides the first investigation on Toxoplasma gondii and Neospora caninum in goats in the Canary Region. Toxoplasma gondii and Neospora caninum presented a low prevalence in the main livestock species on the Canaries. Great disparity was found evaluating the results by island separately for Toxoplasmosis (0–30.4%). Results suggest that semi-desert condition present in many areas of the Archipelago could inhibit the development of Neospora caninum oocysts.