Abstract: This paper studied the degradation performance of fluoxetine by Shewanella oneidensis MR-1 under anaerobic conditions and analyzed the genetic molecular metabolic mechanism from transcriptome. The removal rate of fluoxetine was 93.12% within 12 h, and the degradation rate was 0.94 mg·L^-1·h^-1. The transcriptome sequencing of Shewanella oneidensis MR-1 was performed using the Illumina high-throughput sequencing platform to understand the degradation mechanism of fluoxetine. Profiling and functional analysis of differentially expressed genes for tolerance and fluoxetine degradation using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that envelope stress response membrane protein, ABC transporter, phage shock protein PspA and oxidative stress defense protein played important roles in the tolerance of Shewanella onedensis MR-1 to the environment stress. And the cytochrome C, nitroreductase NfsB and lactate utilization protein played key roles in the degradation and transformation of fluoxetine. This research enhances our understanding of the mechanism of fluoxetine degradation at the transcriptome and suggested a potential application of Shewanella oneidensis MR-1 in environmental remediation.