Introduction. Diabetes mellitus, a condition characterized by chronic hyperglycaemia, is categorized into type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM). Recent research has identified a significant association between diabetes and modifications in the gut microbiota. Gap Statement. Although numerous analyses have been conducted on the gut microbiota of patients with diabetes, regional variations due to factors such as lifestyle and dietary habits remain poorly understood. Aim. This study aimed to compare the gut microbiota structures of adult patients with T1DM, T2DM and healthy controls (HCs) in the Chaoshan region of China, providing theoretical support for gut microbiota-based targeted therapies for diabetes in the Chaoshan region. Methodology. This study enrolled 33 patients with T1DM, 35 patients with T2DM and 30 HCs in the Chaoshan region of China. Faecal samples were collected and subjected to 16S rDNA sequencing and bioinformatics analysis. Results. Our data demonstrated significant variations in gut microbiota diversity among individuals with T1DM, T2DM and HC, accompanied by changes in microbial composition across multiple taxonomic levels. Furthermore, linear discriminant analysis effect size analysis identified distinct dominant species within each group: 27 bacterial genera, including Megasphaera , were significantly enriched in T2DM patients; 27 bacterial genera, including Bacteroides , were significantly enriched in T1DM patients; and 18 bacterial genera, including Alloprevotella , were significantly enriched in the HC group. Metabolic pathway analyses using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Genes (COG) databases demonstrated a significant enrichment of pathways and enzymes associated with starch and sucrose metabolism in both T1DM and T2DM cohorts, compared to HC. Additionally, a diagnostic model based on gut microbiota data at the class level yielded an area under the curve value of 0.861, indicating its high diagnostic efficacy in distinguishing between T1DM and T2DM. Furthermore, an analysis of the abundance of various bacterial phenotypes and probiotic species revealed notable differences among the three groups. Conclusion. This study demonstrates distinct gut microbiota composition, structure and functional profiles in Chaoshan T1DM, T2DM and HC populations, supporting microbiota modulation as a promising therapeutic strategy for diabetes.