Ion channels are involved in the mechanism of anesthetic action and side effect. The transcription and expression of ion channel genes can be modulated by general anesthetics. The adverse effect of continuous infusion of etomidate has been concerned. However, the effects of etomidate on mRNA expressions of ion channel genes remain unclear. In this study, we exposed Daphnia pulex in 250 μmol/L of etomidate for 240 min and observed the change of heart rate, phototactic behavior and blood glucose during the period of exposure, as well as the mRNA expressions of 120 ion channel genes at the end of the experiment. Compared to the controls, heart rate, phototactic behavior and blood glucose were not influenced by 250 μmol/L of etomidate. According to the quantitative PCR results, 18 of 120 Daphnia pulex ion channel genes transcripts were affected by persistent 240 min exposure to 250 μmol/L of etomidate: 2 genes were upregulated and 16 genes were down-regulated, suggesting that etomidate showed effects on many different ion channels in transcription level. Systematical exploration of transcriptional changes of ion channels could contribute to understanding of the pharmacological mechanism of etomidate.