This paper outlines the classification of 82 Indonesian mango cultivars based on morphological characters, RAPD markers (DNA) and a combination of both. Mango cultivars for classification were sourced from Cukur Gondang Collection Garden, East Java. Results, including coefficients of similarity, are presented and discussed for each method of classification: morphological, RAPD markers or the combination of both. The morphological assessment involved 92 morphological characteristics. Results of a cluster analysis provides some detail on the discerning characteristics for each cluster. The results also include a comparison of the clusters and grouping identified through each classification method. The author concludes that the molecular method of RAPD markers and morphological characteristics do not quantify or organise cultivars based on genetic diversity, equally, as the grouping based on RAPD markers produced clusters different to those identified by morphology. The report also concluded that there is wide diversity in Indonesian mango cultivars: 15-62% (morphology), 2-31% (RAPD), and 12-40% (combination of both markers).