In the recently assembled genomes of rice Oryza sativa ssp. indica and japonica, we identified 564 and 519 tRNA genes, respectively. The modified wobble hypothesis, namely, at least 46 tRNA species must present in order to decode all 61 possible anticodons, is perfectly observed in both subspecies. Among the 46 tRNA species, indica and japonica have many identical ones in sequence. There are 18 rice tRNA species that have identical counterparts in Arabidopsis. In the indica superscaffold dataset, 384 5S rRNA genes, dozens of 17S and 5.8S rRNA genes and one 25S rRNA gene were discovered. The incompleteness of observed rRNA genes is mainly caused by the fact that the rRNA genes always exist as tandem arrays in heterochromatic regions that are not successfully sequenced in a whole-genome shotgun approach.