Dissolved nutrients, especially inorganic nitrogen (N) and inorganic phosphorus (P), are typically deficient in the coastal surface waters of temperate regions during warm seasons. Even under the conditions of inorganic N and P deficiencies, the planktonic diatom Chaetoceros tenuissimus sometimes forms blooms. The present study characterized, at the mRNA transcript level, the gene expression patterns in N- or P-limited cultures of C. tenuissimus to propose the molecular markers of N- and P-deficient states of C. tenuissimus. Gene transcriptions of nitrate transporter and glutamine synthetase appeared to be upregulated in N-limited cultures. Phosphate transporter and alkaline phosphatase transcriptions appeared to be induced under P-limited conditions. These results suggest that C. tenuissimus under the N-deficient state expresses a transmembrane nitrate transporter, uptakes nitrate effectively, and assimilates the N source rapidly via glutamine synthesis; P-deficient C. tenuissimus possibly supplements P sources from organic P compounds via hydrolysis actions of phosphatases and uptakes phosphate effectively through phosphate transporters.