We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species 2) high quality chromatin accessibility data for mouse limb development 3) discovery of mass heterochronic genes between fins and limbs 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution. Overall design: RNA-seq analyses of mouse limb and bamboo shark fin development.