Quercus species comprise the major genus in the family Fagaceae and they are widely distributed in the Northern Hemisphere.Many Quercus species including several endemics are distributed in China.Genetic resources have been established for the important genera but few transcriptomes are available for Quercus species in China.In this study,we used Illumina paired-end sequencing to obtain the transcriptomes of two oak species comprising Quercus liaotungensis and Quercus mongolica.Approximately 24 million reads were generated for both species to assemble a total of 103,618 unigenes.A comparison of the transcriptomes of both species identified a total of 12,981 orthologous contigs.