Abstract: To study the algal morphologically based functional group (MBFG) in surface sediments and to understand the density variation of main microalgae population in the ecosystem of sea cucumber shallow water aquaculture pond, the MBFG classification method combined with the redundancy analysis (RDA) was applied to analyse the distribution of microalgae MBFG on the sandy and muddy surface sediments and the relationships between the densities of main functional groups and factors such as water temperature and nutrients. Results showed that the microalgae populations in two different sediments could be classified into two MBFGs,i.e. group Ⅴ and group Ⅵ, which indicated that the microalgae diversity in the sediments was simple. There was only one diatom specie in functional group Ⅵ accordingly. The monthly diatom density in group Ⅵ, which was much higher, was significantly different from that of functional group Ⅴ (p< 0.01). The diatom densities in the sandy and muddy sediments reached peaks of 700 ± 17 cells/cm³ in September and 580 ± 12 cells/cm³ in August, respectively. The diatom densities in the upper 0-2 cm sandy sediments and the muddy sediments were about 3 times and 25 times higher than that in the lower 3-5 cm sediments, respectively. RDA showed that the primary factor influencing the cell density of the MBFG Ⅵ in sandy sediments was active silicate content, while it was water temperature in muddy sediments. The results showed that MBFG classification method could be applied to cluster the microalgae population functional groups in the surface sediments of sea cucumber aquaculture pond and to analyses the density changes of important functional groups when combined with RDA. Therefore, the corresponding management method and maintenance process should be formulated according to the types of sediments in sea cucumber aquaculture ponds during breeding.