In the past decade, microbiome research has rapidly progressed, revealing the critical roles of fecal and oral microbiota in maintaining internal homeostasis. Studies employing 16S rRNA and metagenomics have highlighted dysbiosis of the fecal and oral microbiota as closely linked to PCA development and progression. However, significant gaps exist in understanding the fecal and oral microbiota in patients with pancreatic cancer (PCA) versus benign or low-grade malignant pancreatic tumors (NPCA). This study aimed to analyze fecal and oral microbiota characteristics, and to establish classifiers to discriminate PCA from NPCA, providing a reference for early clinical identification of malignant tumors.