Sixty-three mandarin (Citrus spp.) cultivars from the collection of the Campo Citrícola Experimental Francisco Villa, Tamaulipas, Mexico, were evaluated using morphological and Amplified Fragment Length Polymorphism (AFLP) markers. Twenty quantitative and 10 qualitative morphological characters from leaves, flowers and fruits were evaluated. The Mse +CAG plus Eco +ACA, and Mse + CAA plus Eco + AGG AFLP primers were the best combinations and generated 109 bands with 86% polymorphism. Both morphological and molecular analysis showed a high degree of variation among analyzed accessions, indicating an important source of genetic diversity that can be used in future breeding programs. Although comparison of morphological and molecular data using the Mantel test did not indicate a significant correlation (r= 0,31), both techniques appeared to be complementary for mandarin characterization.