This study describes the population genetic structure of Milicia species sampled from different provenances distributed over 5 countries (Sierra Leone, Cote d'Ivoire, Ghana, Cameroon and Tanzania). Random amplified polymorphic DNA (RAPD) and inter sample sequence repeats (ISSR) variation in 41 accessions from 5 different populations were consistent with each other. Analysis of molecular variance partitioned RAPD and ISSR variation into within- and between-population components. The between-population variation component was large, accounting for 62.2% and 71.5% for RAPD and ISSR respectively. Dendrogram analysis produced 2 major clusters separating dry zone accessions (mainly M. excelsa) from moist/wet zone accessions (mainly M. regia). Sub-clustering further separated accessions by forest type and/or geographic region. Phylogenetic analysis of chloroplast genes involved the use of nucleotide sequencing, restriction fragment length polymorphism (RFLP), and microsatellites. Only one region (5' to trnS) out of 6 regions analysed was polymorphic and revealed 3 different cytotypes. The distribution of the cytotypes matched with the 2 major clusters produced by the dominant markers. Wet/moist and dry zone bands were identified with little evidence of gene flow between populations. Seed mediated gene flow estimated from the chloroplast analysis was small (Nm = 0.23). To relate these molecular information with Phytolyma resistance, field provenance and progeny trials were conducted. Accessions from wet/moist zones were more tolerant to Phytolyma than accessions from dry zone. The data also suggest that accessions bearing the wet/moist zone specific markers have a high probability of being tolerant to Phytolyma. The approaches outlined and the results have general applicability in the sustainability of Milicia spp. and are discussed in relation to germplasm sampling, management and conservation of genetic recourses of Milicia species.