Micropropagation of oil palm by somatic embryogenesis produces a proportion of off-type individuals (approximately 5% overall) displaying a homeotically modified flower structure known as mantled. Transformation of the fertile or sterile androecium into carpel-like structures is observed in staminate and pistillate mantled flowers, respectively, resulting in lower oil yields in affected plantations. Given the epigenetic nature of the mantled condition, a gene expression-based approach was used rather than a genetic one to investigate its molecular basis. Suppression subtractive hybridisation (SSH) and macroarray hybridisation were used to compare transcriptome patterns between normal and mantled inflorescences. Two SSH libraries, enriched for complementary deoxyribonucleic acids (cDNAs) of either true-totype or somaclonal variant material, were generated. Bioinformatic analysis of these two libraries allowed the identification of 1,350 unique sequences and their annotation by a gene ontology-based approach. Macroarray hybridisation was used to compare gene expression between normal and mantled inflorescences, and 32 genes were found to be differentially expressed. The temporal expression patterns of six genes were further investigated in more detail in relation to male and female inflorescence development. Full-length cDNAs were isolated and characterised for two of these genes, EgFB1 and EgRING1, both of which are down-regulated in the mantled inflorescences and both of which encode proteins associated with proteolytic signalling complexes. Our data shed light on gene expression changes associated with the mantled phenotype and have provided novel transcriptome markers which can help to distinguish the abnormal and wild-type inflorescences.