Abstract Background: There is currently no optimal sampling method for upper gastrointestinal (UGI) tract microbiota. We compared biopsies and mucosal swab specimens for microbial sampling from patients with UGI carcinoma. Methods: A total of 67 patients with esophageal squamous cell carcinoma (ESCC) and 36 patients with gastric cardia adenocarcinoma (GCA) were recruited in the Linxian Cancer Hospital (Henan, China). Sterile biopsies and swabs were used to collect paired samples from the resection specimens from carcinoma and adjacent normal tissue. Data from 16S rRNA gene sequencing were processed using QIIME2 to evaluate differences in alpha and beta diversity and taxonomic relative abundances between specimen types. Results: Alpha diversity was not significantly different between swab specimens and biopsies, both for ESCC and GCA. Paired specimens were correlated for both sample types from ESCC (ρ > 0.6, P < 0.001) but not GCA (ρ < 0.4, P > 0.05). For beta diversity, distinct clustering by sampling method was not observed for adjacent normal or tumor tissue from ESCC or GCA. There was a high correlation for weighted UniFrac and Bray–Curtis distance only in ESCC paired specimens (ρ > 0.6, P = 0.001). The 10 dominant bacterial genera were similar between swab and biopsy specimens. However, higher levels of Veillonella (P = 0.0002) and Streptococcus (P = 0.0002) were detected in ESCC adjacent normal and GCA carcinoma swabs, respectively, compared with the biopsies. Conclusions: Mucosal swab specimens and biopsies could yield similar microbial profiles from ESCC but not GCA. Both can be used to characterize UGI microbiota; one sampling method should be selected for future studies. Impact: This study provides insight for planning microbiota collections from the UGI tract.