To characterize the ultraphytoplankton community structure and understand its succession, we investigated photosynthetic pigment concentration and composition; algae phyla composition and abundance; and environmental factors in Xiangxi Bay (XXB) from February to December 2013. High-performance liquid chromatography (HPLC) analyses revealed eight diagnostic pigments: Fucoxanthin, Neoxanthin, Violaxanthin, Alloxanthin, Lutein, Zeaxanthin, Chlorophyll b and Chlorophyll a. The temporal differences between seven of the pigments (all excepting Neoxanthin) were significant (P < 0.05), and there were no significant spatial differences between the eight pigments (P > 0.05). A chemical taxonomy (CHEMTAX) calculation identified seven phyla of ultraphytoplankton: cryptophytes, chlorophytes, cyanobacteria, diatoms, euglenophytes, chrysophytes, and dinoflagellates. The temporal differences between five of the phyla (except chlorophytes and euglenophytes) were significant (P < 0.05), and there was no significant spatial difference between the seven phyla (P > 0.05). The redundancy analyses demonstrated that the key environmental factors for the succession were N-NH 4 C and P-PO 4 3-. Application of the HPLC-CHEMTAX method has provided the first analysis of ultraphytoplankton community structure in XXB, and our findings also show that environmental factors influence the succession of ultraphytoplankton over time.