Sea cucumber (Apostichopus japonicus) is one of the most important economic aquaculture species in China. The study on the genome size(C-value) is highly significant because it plays an important role in instructing the hybridization breeding and improved variety breeding program, as well as in estimating the cost of the whole genome sequencing project. Previous studies mainly focused on these research areas such as ecology, physiology, nutrition etc. However, it is relatively scarce for the accumulation of basic data related to the genome size and characteristics in A. japonipus. Therefore, the measure of genome size for enriching cytogenetics data of this species is meaningful. In this paper, the genome size(C-value) of sea cucumber, A. japonicus was measured through flow cytometry in 52 individuals, which came from aestivation, normal and wild groups, using erythrocyte DNA content of chicken, Gallus domesticus(2.5pg/2C) as internal standard. The result indicates that the C-value of A. japonicus is (0.90± 0.06) pg, equivalent to (880.2±72.26) Mb. And,the C-values of aestivation, normal and wild are (0.93±0.05) pg, (0.90±0.05) pg and (0.84±0.02) pg, respectively. In addition, analyzed by Independent-Samples T Test, it shows that the C-values have no significant difference in aestivation and normal groups, whereas, the C-values of wild group and that reared in captivity group have significant difference. In other words, there is no correlation between genome size and the physiology factor-aestivation, while the stability of environment factors has certain influences on genome size variation. Moreover, the development of C-value measure method was elucidated in detail, in the meanwhile, the relationship between C-value and the evolution in Holothuroidea was discussed in combination with genome size of other types of sea cucumber.