Genetic structure in the resting-egg bank of the rotifer Brachionus calyciflorus were investigated in Xihai pond, Beijing, using segmental mitochondria cytochrome c oxidase subunit I (COI) gene (543bps) as the marker. We got a total of 6 haplotypes in 46 clones hatchling from the sediment collected in April. To make further insight into the genetic differentiation of the resting-egg bank, we selected four haplotype clonal groups with higher frequency to compare their fitness characteristics and body size at different food (Chlorella pyrenoidosa) density of 1×106 cells/ml, 6×106 cells/ml and 12×106 cells/ml (temperature: 25℃) or under different temperatures of 15℃, 25℃ and 35℃ (food: 6×106cells/ml), respectively. Both the interactions of haplotype vs. food (R0: P=0.038; rm: P=0.027) and that of haplotype vs. temperature (R0: P=0.006; rm: P=0.000) had obvious effect on growth reponses of the clonal groups. Moreover, there was significant interaction of haplotype vs. temperature (lorica length: P=0.033; lorica width: P=0.000) and haplotype vs. temperature (lorica length: P=0.027; lorica width: P=0.000) on body size of the clonal group. Combining with the life table and body size data, niche differentiation and morphodifferentiation of the clonal groups and the possible influence on the population structure dynamics were discussed. Key Words: rotifer Brachionus calyciflorus; resting egg bank; genetic diversity; differentiation; population growth; body size