The goal of this study was to conduct gene expression profiling, using transcriptome sequencing, of tissue samples from green sea turtle (Chelonia mydas) with and without fibropapilloma tumors. With the primary aim of identifying genes aberrantly expressed in fibropapilloma tumors we sequenced blood, normal skin tissue, and tumor samples from turtles with and without fibropapilloma. Total RNA was extracted from tumor and healthy tissue samples, after homogenization, using a Qiagen AllPrep DNA/RNA Mini kit, according to the manufacturers instructions. Total RNA was extracted from blood samples using PAXgene blood RNA kit from Qiagen. 48 samples, comprising 13 blood samples, 26 fibropapilloma tumor samples and 9 non-tumor samples from 12 juvenile turtles (C. mydas) were used for sequencing. Sequencing libraries were prepared from up to 250ng of total RNA using a KAPA RNA HyperPrep kit (Roche Diagnostics) with polyA selection and indexed using a KAPA Dual-Indexed adapter kit (Roche Diagnostics), according to manufacturers instructions. Libraries were pooled for paired-end 100bp sequencing on a HiSeq 2500 system (Illumina).