To understand how a biological population established in a novel habitat, it is important to know temporal genetic dynamics of the population. In this research, we examined the change of genetic structure from the early phase of the establishment of an obligated parthenogenetic Daphnia pulex population, using their dormant eggs preserved in the varved sediments. In Lake Fukami-ike (Nagano Prefecture), we collected sediment core samples and conducted population genetic analysis using dormant eggs on the sequence of 1628 bp of mtDNA. D. pulex established a firm population in early 2000s. Population genetic analysis suggested that one haplotype was dominant throughout the study period with no turnover and no increasing genetic diversity. Analyses of morphological traits suggested that body size and defensive traits changed in response to predator community change, whereas genetic structure showed little change during the corresponding periods. In addition, statistical analysis suggested that the responses to nutrient concentration and predator community differed haplotype to haplotype. The direction and degree of the responses were opposite between the dominant haplotype and other haplotypes that were genetically distant from the dominant one. In conclusion, a biological population might success to colonize and adaptively respond to new habitat with limited genetic diversity.