The functional diversity of microbial communities in sediment and shelter of sea cucumber (Apostichopus japonicus) cultural ponds was examined in this paper. The BIOLOG method and redundancy analysis (RDA) were used to evaluate seasonal changes and their relationships with environmental factors. The results showed that both total amount and types of carbon sources utilized by sediment and shelter microbes in sea cucumber cultural ponds varied seasonally, and was higher in spring, summer and autumn as compared with those of winter. The main types of carbon sources utilized were polymers, carbohydrates, carboxylic acids and amino acids by sediment microbes, and polymers, carbohydrates, amino acids and amides by shelter microbes, respectively. Principal component analysis revealed that carbon metabolism functional diversity of sediment and shelter microbial communities in sea cucumber cultural ponds varied significantly over the seasonal courses. For sediment microbes, 18 categories of carbon sources were significantly related to the principal components, of which some related to principal component 1 were carbohydrates, carboxylic acids and amino acids, and others related to principal component 2 were polymers and carbohydrates. For shelter microbes, 22 categories of carbon sources were significantly related to the principal components, of which some related to principal component 1were polymers, carbohydrates, carboxylic acids and amino acids, and others related to principal component 2 were carboxylic acids. Significant seasonal changes were detected for all microbial diversity indexes including Shannon, McIntosh, Simpson and S-E in sediment and shelter of sea cucumber cultural ponds, but differences were also observed in seasonal variations between microbial diversity indexes. RDA analysis revealed that TP, NO₃-N and PO₄-P were the critical factors influencing seasonal changes in sediment microbial community functional diversity, while SOM, NO₃-N and TN were the critical factors influencing seasonal changes in shelter microbial community functional diversity. In conclusion, seasonal changes in microbial community functional diversity were marked and different in sediment and shelter of sea cucumber cultural ponds, and this correlated well with environmental factors.