Propofol is multiple influences on organism function that could affect gene expressions of ion channels, cause arhythmia, impair brain cognitive functions, inhibit energy metabolism and increase hypoxic tolerance. To evaluate whether these phenomena might still exist in persistent low concentration of propofol exposure. We investigated changes in the mRNA levels of Daphnia 120 ion channel genes in response to exposed to persistent propofol (25 mM) for 240 min using quantitative PCR techniques. The heart rate (HR), glucose levels, phototactic behavior and hypoxic tolerance were recorded during the experiment. Sixteen of 120 ion channel transcripts in Daphnids were affected by propofol exposure: among them, 4 ion channel (1 Voltage-gated potassium (Kv) channel and 3 Ca2+-activated Cl- channels) genes were upregulated and 12 ion channel (3 Kv channels, 1 Cyclic nucleotide-gated channel, 1 Transient Receptor Potential Channel, 1 Glutamate-gated ion channel, 3-aminobutyric acid type A receptors, 1 DEG/ENaC channel, and 1 inositol 1, 4, 5-trisphosphate receptor) genes downregulated. Propofol did not show effect on gene expressions of Voltage-gated Calcium channels, Voltage-gated Sodium channels, Sodium-leak channel, Two-pore calcium Channel, AMPA receptor, NMDA receptor, Glutamate-gated chloride channels, Histamine-gated chloride channels, ATP-gated ion channels, Calcium release-activated calcium channel, Chloride intracellular channel, Bestrophin, Tweety channel and anoctamin. Additionally, propofol exposures not infuence HR, glucose levels, phototactic behaviors or hypoxic tolerances. Persistent propofol exposure even in small doses could affect multiple ion channels at mRNA levels. Systematical exploration of transcriptional changes of ion channels contributes to provide some insights into the understanding the mechanism of propofol.