Analysis of gene expression commonly uses internal control gene for normalization. The mRNA levels for cytb and β-actin genes were detected by using RT-PCR at 11 larval development stages of sea cucumber(Apostichopus japonicus)including unfertilized egg, fertilized egg, cellulous stages, blastula, gastrula, early auricularia, auricularia, late auricularia, doliolaria, pentactula, juvenile and in different tissues of young sea cucumbers including body walls, coelomocytes, intestines and respiratory trees. The results showed that cytb gene expression was stable at all development stages and in the four tissues. The mRNA levels for β-actin gene showed significant differences at different development stages, but were stable in the tissues of body walls, intestines and respiratory trees. Moreover, cytb mRNA showed no significant changes in expression after a LPS challenge at the stages of gastrula, early auricularia, auricularia, late auricularia, doliolaria and juvenile or in the four tissues of young sea cucumbers. The expression of β-actin gene was also stable in the tissues of coelomocytes, intestines and respiratory trees after a LPS challenge. This study provides information for the selection of cytb gene and β-actin gene as suitable internal control gene in target genes expressions research of sea cucumber.