This mRNA-Seq was performed to obtain the basic genetic information of the early embryonic development in medaka, Oryzias latipes. The samples of total RNA were extracted from medaka fertilized eggs at 0, 1, 3, 5, 7 dpf (days post fertilization), and paired-end reads mRNA sequence was performed. Medakas of these samples are Oryzias latipes and normal phenotype. day0_1.fastq.gz and day0_2.fastq.gz are obtained from the 0 dpf sample, day1_1.fastq.gz and day1_2.fastq.gz are from 1 dpf sample, day3_1.fastq.gz and day3_2.fastq.gz are from 3 dpf sample, day5_1.fastq.gz and day5_2.fastq.gz are from 5 dpf sample and day7_1.fastq.gz and day7_2.fastq.gz are from 7 dpf sample.