The Citrus EST sequences in public databases total 562,490, belonging to different species or hybrids. Citrus sinensis L. Osbeck is the most well represented member of the group. We have done RNA seq (Illumina) and generated a set of approximately 350 million Illumina reads (101 bases) for C. sinensis and 70 million reads for C. reticulata that we are currently being used for re-assembling unigenes. A previous set of sweet orange unigenes, with 38,781 different members was used for comparing the genomes of C. sinensis, C. clementina, C. reticulata, C. limonia, and P. trifoliata in relation to presence of introns in the genes. The gmap software (http://www.gene.com/share/gmap) was used for identifying exons in the genomes. The unigenes that presented coverage of at least 90% in at least three genomes were further analyzed, identifying the ones that were differently distributed in the genomes and confirming the existence of the introns by blastn analysis. From the starting set we identified forty-six unigenes with structural differences among the genomes analyzed. The majority appeared just in the C. sinensis genome assembly, thirty-five of them but just two seems to be real since the others were just sequences of n. This work allowed us to identify genes that present structural differences among the genomes. These genes have different functions, and the presence/absence of the intron may have biological implications since they may have regulatory functions but that remains to be further evaluated. Financial support: INCT Citros (Fapesp and CNPq) and Embrapa.