This phenological analysis of bitter and sweet bush mango trees is part of their biosystematics. It supports the species distinction hypothesis postulated by Harris (Bull J Bot Nat Belg 65(1–2):143–196, 1996 ) and Lowe et al. (Mol Ecol 9:831–841, 2000 ). African Bush Mango trees are priority food trees in Sub-Saharan Africa. The unclear distinction between bitter and sweet fruited trees is still subject to taxonomic debate. This hinders their effective use and conservation programmes. This study investigates differences in phenological behaviour between bitter and sweet fruited populations and their taxonomic implications. Monthly phenological description data on seven populations of bitter or sweet bush mangos across Benin and Togo were used to assess within and between mango type phenological diversity, to discriminate bitter and sweet trees and to evaluate their responses to environmental factors. The phenological states differentiating bitter and sweet trees were identified and individual trees were classified based on the discriminating phenological characters. Finally, phenological variation was analyzed with time of the year, soil type, type of bush mango tree, and climatic zone. Phenological diversity varies significantly among populations. Bitter and sweet trees have consistently different phenological states. Bitter trees have a lower phenological diversity for all phenological phases throughout the year compared to sweet trees, possibly due to their limited distribution range in the study area. The tree types also differ in their reproductive responses to environmental factors, but did not respond differently to soils. These results support the hypothesis that bitter and sweet trees represent different taxa and we suggest for efficient conservation purpose to consider them as different species.