Free-living zooxanthellae, much like symbiotic zooxanthellae, contribute to maintaining the health of the coral community. Previous studies have shown that Symbiodinium sp., a free-living zooxanthellae, exhibits different responses to various phosphate concentrations in terms of growth and alkaline phosphatase activity. To understand how Symbiodinium sp. responds to dynamic changes in dissolved inorganic phosphorus (DIP), we carried out comparative analyses on the transcriptome of this dinoflagellate under two different initial phosphate concentrations in 0, 5, and 10 d. Initial phosphate concentrations of 0.15 and 35 μmol/L were designed based on the phosphate concentration of an F/2 medium typically used in laboratory culture and a low average phosphate concentration of the East China Sea in recent years, respectively. The de novo assembly results showed that 231 642201 Transcripts and 80955 Unigenes were obtained; a total of 4407 (5.44%) Unigenes were co-annotated in the NR, gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), evolutionary genealogy of genes: non-supervised orthologous groups (eggNOG), SwissProt, and protein families (Pfam) databases. In addition, 27 236 (33.64%) Unigenes had significant matches in the NR database. All Unigenes annotated in the NR database were selected for annotation in the GO database. As such, a total of 23998 (29.64%) Unigenes were mapped into three categories: molecular function, cellular population, and biological process. Among the annotations in the GO database, there were 13 sub-categories of molecular functions, 16 sub-categories of cellular components, and 19 sub-categories of biological processes. The eggNOG functional analysis results showed that 45387 (56.06%) Unigenes were divided into 25 categories according to their functional characteristics. The largest category was post-translational modification, protein turnover and chaperone (3704, 8.16%), followed by signal transduction mechanism (3272, 7.21%), translation, ribosomal structure and biological development (2091, 4.61%), extracellular structure (168, 0.37%), nuclear structure (78, 0.17%), and cell movement (24, 0.05%). To obtain the differentially expressed genes related to phosphorus utilization, transcriptome data from five experimental groups were compared and analyzed. The results suggest that there were three phospholipase A2 genes, two phospholipase B genes, one phospholipase C gene, three phospholipase D genes, two alkaline phosphatase, genes, four acid phosphatase genes, three inorganic phosphate transporter genes, two sodium-dependent phosphate transporter genes, and three mitochondrial phosphate transporter genes that were differentially expressed. According to the genetic expression profile of the differentially expressed genes, it was hypothesized that the free-living Symbiodinium sp. may continue growing under low phosphorus stress by enhancing its ability to transport inorganic phosphate into cells and utilizing organic phosphorus via phosphatase. This study improves the current understanding on the survival mechanism of zooxanthellae in oligotrophic seas. The findings pave an avenue to uncover the molecular regulation mechanism of Symbiodinium sp. in response to different phosphate concentrations.