Chronic multi-symptom illness (CMI) affects a subsection of elderly and war veterans and is associated with systemic inflammation, chronic fatigue, pain and neuroinflammation. We showed previously that an altered gut microbiome-inflammation axis aids to the symptom reporting and persistence. Here, a mouse model of CMI and a group of Gulf War veterans’ with CMI showed the presence of an altered host resistome, a signature of antibiotic resistance genes within the microbiome. Results showed that antibiotic resistance genes were significantly altered in the CMI group in both mice and GW veterans when compared to the control. Fecal samples from GW veterans with persistent CMI showed a significant increase of resistance to a wide class of antibiotics and exhibited an array of mobile genetic elements distinct than normal healthy controls. Strikingly, the altered resistome and gene signature were correlated with mouse serum IL6 levels. Altered resistome in mice also correlated strongly with intestinal inflammation, decreased synaptic plasticity that was reversible with fecal microbiota transplant (FMT), a tool to restore a healthy biome. The results indicate an emerging linkage of the gut resistome and CMI and might be significant in understanding the risks to treating hospital acquired infections in this population.