Annona senegalensis Pers. is one of the wild fruit tree for domestication in southern Africa. An assessment of the genetic diversity in A. senegalensis would assist in planning for future germplasmcollection, conservation and fruit domestication programmes. During 2004 to 2006 nine populations were collected from different locations in Malawi and genetic diversity was evaluated using microsatellites or simple sequence repeats (SSRs) developed in Annona cherimola. In total 23 alleles were detected in the populations studied and genetic diversity parameters revealed high levels of heterozygosity with 4.0 to 14 alleles per locus and the populations were genetically different by 19% as given by the value of theta. Results demonstrated association between genetic and geographical distance in the species indicating that large-scale geographical and ecotypic differentiation wasreflected by the SSR markers. The high genetic diversity is attributed to biological characteristics of the tree species and habitat heterogeneity. The study has revealed evidence of application of SSR markersfrom A. cherimola towards genetic fingerprinting of A. senegalensis. Implications of the SSR marker data for optimizing genetic management of the species are discussed
