The ‘Philippine Lono Tall’ (PLNT) is a variant of the more common ‘Philippine Laguna Tall’ (LAGT), which produces fruits with soft endosperm and reported higher fat content. To understand patterns of fatty acid (FA) and oil accumulation in LAGT and PLNT fruits, transcriptomes of 6–7 month-old endosperm samples were analyzed by RNA-Seq. This first report of the complete ontogenetic FA profile revealed that medium chain fatty acids are the main components of oil from the PLNT endosperm. This pilot study is the first to suggest a molecular basis for the unique ‘Lono’ phenotype.