A large Elaeis guineensis microsatellite development program has been undertaken to generate wide range of (GA)n, (GT)n and (CCG)n Simple Sequence Repeats (SSR) markers useful for oil palm genetic mapping, genetic diversity study and variety identification. Comparative results building several microsatellite-enriched libraries demonstrate that an optimised hybridization and capture methodology, using biotin-labelled microsatellite oligoprobes and streptavidin-coated magnetic beads, is the quickest and best adapted procedure to ensure a high enrichment rate with minimal redundancy. A set of 21 SSR loci are evaluated with estimates of the size range and expected heterozygosity in E. guineensis as in the close related E. oleifera as where an optimal transportability of the SSR markers was observed. SSR mendelianation allows oil palm breeders to use SSR markers for genetic mapping and for the of agronomic genes based on both intra- or inter-specific progenies. Multivariate data is show the ability of our developed SSR markers to reveal the genetic diversity structure E. guineensis and E. oleifera natural populations, in accordance with already measured ships and with geographical origins. Very high levels of allelic variability indicate that it will be a powerful tool for variety identification in the Elaeis species.