Objective To investigate the gut microbial characteristics in patients with acute ischemic stroke and resilience of the gut microbiota after a stroke. Methods Ninety-five fecal samples from 28 ischemic stroke patients and 28 fecal samples from 28 healthy volunteers were collected.DNA was extracted from these samples and the bacterial 16S rRNA were amplified through real-time quantitative polymerase chain reaction (qPCR). All PCR products were mixed together and then sequenced using the Illumina Hiseq 2500 platform. Microbiome analysis was implemented in QIIME. Results Patients with acute ischemic stroke showed significantly higher diversity than controls (phylogenetic diversity, P=0.002). The overall composition of the gut microbial communities also differed significantly between acute ischemic stroke patients and healthy controls as indicated by the clear separation in principle coordinate analysis (Adonis test on Bray-Curtis, P<0.001). Stroke patients' intestines had more opportunistic pathogens, such as Enterobacteriaceae, Veillonellaceae and Streptococcaceae, fewer commensal or beneficial genera including Bacteroides and Prevotella. Four weeks after onset, the gut microbiota in stroke patients began to restore, but the alpha diversity declined (P<0.05). Conclusion The present study has revealed the characteristic of gut microbial dysbiosis and recovery in acute ischemic stroke patients.However,the significance of the dynamic gut microbiota in stroke patients needs further study.