Mollusks have received increasing interest in ecotoxicological studies but so far the available scientific analyses of how their genes are affected by anthropogenic pollutants are scarce. The focus of this study is to identify an estrogen receptor (er) gene in the common prosobranch snail Bithynia tentaculata and to test a hypothesis that 17α-Ethinylestradiol (EE2) will modulate er gene expression after short-term exposure. We set up exposure experiments with a total of 144 snails, which were collected from a natural population in southern Sweden. Snails were exposed to either 10 ng/L or 100 ng/L EE2 during 24 h and/or 72 h. From the isolated B. tentaculata RNA we successfully identified and characterized a novel er gene and phylogenetic analyses strongly indicate that the Bithynia er gene is an ortholog to the human ERα (ESR1, NR3A1). We found a significant interaction between EE2-dose and exposure duration on the er's gene expression (Two-way ANOVA; p = 0.04). We also found a significant difference in the gene expression of the er when comparing the control and 100 ng/L treatment groups after 72 h in female snails (One-way ANOVA; p = 0.047). The results from this study should be useful for future field-related studies of estrogen receptors in natural populations of mollusks.