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The partial sequence of Skeletonema costatum proliferating cell nuclear antigen (PCNA) gene was obtained by RT-PCR. A 714 bp cytochrome b (Cyt b) gene fragment of S.costatum was cloned for the first time. Based on the cloned sequences, a FQ-PCR method was developed to detect the S.costatum PCNA and Cyt b gene, respectively. The above method was applied to study the relationship between the S.costatum growth rate mu(d-1) and the average expression amount of PCNA gene in a single cell. The expression amount of PCNA gene had large variation in different culture phases, and the trend was well consistent with the growth rate, which suggested that the expression amount of PCNA gene correlated well with the cell division, and the PCNA might be a promising indicator for the S.costatum cell proliferation. While the expression amount of Cyt b gene had no obvious variation during different culture phases, which indicated that the Cyt b was a good potential house-keeping gene. Furthermore, using the PCNA gene as the objective gene and the Cyt b gene as the house-keeping gene, a new approch for estimating the S.costatum in-situ growth rate was established by the relative expression quantity (REQ) of the PCNA gene.