<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Legitimacy in breeding and commercial crop production depends on optimised protocols to ensure purity of crosses and correct field planting of material. In oil palm, the presence of three fruit forms permits these assumptions to be tested, although only after field planting. The presence of incorrect fruit forms in a cross is a clear sign of illegitimacy. Given that <jats:italic>tenera</jats:italic> forms produce 30% more oil for the same weight of fruit as <jats:italic>dura</jats:italic>, the presence of low levels of <jats:italic>dura</jats:italic> contamination can have major effect during the economic lifespan of an oil palm, which is around 25 years. We evaluated two methods for legitimacy test 1) The use of SHELL markers to the gene that determines the shell-thickness trait 2) The use of SNP markers, to determine the legitimacy of the cross.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>Our results indicate that the SHELL markers can theoretically reduce the major losses due to <jats:italic>dura</jats:italic> contamination of <jats:italic>tenera</jats:italic> planting material. However, these markers cannot distinguish illegitimate <jats:italic>tenera</jats:italic>, which reduces the value of having bred elite <jats:italic>tenera</jats:italic> for commercial planting and in the breeding programme, where fruit form is of limited utility, and incorrect identity could lead to significant problems. We propose an optimised approach using SNPs for routine quality control.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Both <jats:italic>dura</jats:italic> and <jats:italic>tenera</jats:italic> contamination can be identified and removed at or before the nursery stage. An optimised legitimacy assay using SNP markers coupled with a suitable sampling scheme is now ready to be deployed as a standard control for seed production and breeding in oil palm. The same approach will also be an effective solution for other perennial crops, such as coconut and date palm.</jats:p> </jats:sec>