We conducted an exhaustive study of gene expression in fig fruits to identify the gene complexes responsible for fundamental fruit physiology and phenotypic differences between ecotypes. We performed high-throughput pyrosequencing on cDNA libraries constructed from caprifig and common fig fruits and compared their transcriptomes by analyzing the expressed sequence tags obtained. We collected a total of 290,594 expressed sequence tag reads from the two fruit types and assembled them into 71,455 unigenes (19,166 contigs and 52,289 singletons). We identified many metabolic genes, including those encoding proteins in the ethylene, glucose, and anthocyanin synthesis pathways that are involved in fruit maturation. This set also contained unigenes with unidentified functions. We observed no significant differences between the fruit types with respect to Gene Ontology term representation. By reverse transcription polymerase chain reaction, however, we detected several polymorphisms at the level of individual genes. Inter-type variations with respect to the expression level or transcription product size were observed in B- and C-class MADS-box gene homologs and chalcone synthase homologs, which are believed to be involved in sexuality and parthenocarpy, respectively. Expression polymorphisms were also observed for other genes, including a gibberellin-regulated protein gene. Our data and results contribute to genetic research on fig fruits and will aid in the understanding of fruit physiology and mechanisms of phenotypic differentiation. © 2013 Springer-Verlag Berlin Heidelberg.