Numerous studies have revealed distinct differences in the profiles of gut microbiota between non-obese (NO) and obese (OB) individuals. To date, however, little is known if any disparities in the community of gut microbiota exist between metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) subjects. We therefore aimed to comprehensively characterize the gut microbiota and circulating metabolites in serum from both MHO and MUO residing in the remote island, Kumejima, where the prevalence of obesity is one of the highest in Japan, and explored possible correlations between the gut microbiota profile and markers of metabolic syndrome. In our data, MUO showed significantly higher levels of g_Paraprevotella, g_Cloacibacillus, g_Atopobium and g_Megasphaera in comparison to MHO. MUO also showed significantly lower levels of g_Holdemania, f_Ruminococcaceae;g_Ruminococcus, g_Eggerthella, g_Phascolarctobacterium and f_[Mogibacteraceae];g_ as compared to MHO, with a number of these genera negatively correlating with value of circulating triglyceride, total-cholesterol and LDL-cholesterol. In contrast to MHO, MUO showed an imbalance of serum metabolites, with a significant elevation in 2-oxoisovaleric acid, pyruvic acid, 2-hydroxybutyric acid, and creatine. Our data highlight unmet needs in precision approaches for the treatment of obesity, targeting the gut microbiota profile and serum metabolites in a distinct population affected by obesity.