Abstract: To select the reference genes applicable for 17 development stages and 7 tissues of Ruditapes philippinarum, expression stabilities of elongation factor 1 alpha gene (EF1A), TATA-box binding protein gene (TBP), histone gene (HIS), cytochrome b5 gene (CYTB5), ubiquitin-conjugating enzyme gene (UCE), ribosomal protein L8 gene (RPL8), ribosomal protein S23 gene (RPS23), ribosomal protein L2 gene (RPL2), cytochrome C gene (CYTC), growth factor receptor-bound protein 2 gene (GFRP2), β-actin gene (ACT) and tubulin gene (TUB) were then evaluated with three algorithms—geNorm, NormFinder and ΔCt methods, respectively. The results suggest that CYTC, CYTB5 and RPS23 were the optimal reference gene combination for different development stages; CYTB5 and GFRP2 were recommended for qRT-PCR normalization of different tissues. The ACT was proved to be the most unstable in different development stages and different tissues of R. philippinarum.