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.