Despite the ecotoxicological value of the freshwater ostracod Heterocypris incongruens, there is little nucleotide sequence information on this species. With the aim to develop transcriptome resources of this species, we performed a de novo transcriptome analysis using a high-throughput sequencing technology and determined the sequences of antioxidant gene, such as catalase (cat), glutathione peroxidase (gpx), glutathione S-transferase C-terminal domain-containing protein (gstcd), and superoxide dismutase [Cu-Zn] (sod). To provide an application example of expression analyses using the obtained genes, we examined the expressions of the obtained genes by quantitative PCR (qPCR) in H. incongruens exposed to urban road dust, as a model of contaminated environmental sample. The expressions of all the target genes remained unchanged in response to road dust during six days of exposure. Our transcriptome data and sets of stress response genes of H. incongruens should be useful references to investigate the mechanism of sediment toxicity and to aid linkage between environmental contamination and biological responses.