The tropical rainforests of Africa and Madagascar show huge biodiversity characterized by great species richness and endemicity. In such context, for the genera that experienced radiative speciation, phenotypic divergence can be important while the associated genetic differentiation could remain low. It results in low congruency between genetic and phenotypic diversity. Actually, 58 and 47 Coffea species (excluding ex-Psilanthus genus and Baracoffea groups) respectively from Madagascar and Africa were described (although three and seven species from Madagascar and Africa respectively are not yet formally recognized). These Coffea species show a high phenotypic diversity in term of phenological traits, fruit size and color, fruit maturation time, tree height, biochemical composition of leaves and fruits, and indeed genetic diversity.

Recently, a completely resolved molecular phylogenetic tree was obtained using 28,800 concatenated Single-Nucleotide Polymorphisms (SNPs) markers obtained from Genotyping-By-Sequencing (GBS) methodology (Hamon et al., 2017).

The necessity to use GBS for assessment of between-species genetic divergence could be explained by two non-exclusive mechanisms:

1) the absence of strong genetic barrier and therefore the maintenance of gene flow between species even at a low rate and

2) recent speciation coupled with rapid morphological divergence.

In this section, we present some recent studies describing the huge diversity of Coffea species at the phenotypic and genetic levels. Our current project include now the analysis of species not included into living collections.