The “shell thickness” gene (Sh) controls three fruit types in African oil palm [Elaeis guineensis (Eg)] and has important implementations for variety development. Eg plantations in South and Central America suffer severally from the “Pudrición de Cogollo” disease, leading to the development of hybrid varieties between African and American oil palm [E. oleifera (Eo)]. We have analysed the allelic variation of a 237 bp amplicon within the Sh gene in Eo, interspecific hybrids and Eg pisifera accessions. A total of 568 accessions from different geographical origins were screened. Seven SNP were detected. Three SNP correspond to already known SNP from Eg, defining the dura, pisifera Congo, pisifera Nigeria and MPOB3 events. Further downstream in an intronic region revealed four novel additional SNP which occur only in Eo alleles. Three specific Eo events (OLI1, OLI2 and OLI3) were defined. The allelic composition for the partial Sh amplicon was determined in all accessions and specific associations between origins and Eo events were detected. SNP NK2 was specific for all Eo alleles and absent in Eg, allowing the design of species specific primers. These were validated successfully in all screened accessions and are crucial for selecting appropriate genotypes in backcross programs with interspecific hybrids. The effects of origin and Sh alleles on fruit weight and fruit components were analysed in Eo accessions and hybrids. For the Eo alleles no effects were detected on these traits, while the origin influenced significantly trait expression in most cases.