STAMP (Statistical Analysis of Taxonomic and Functional Profiles) is a graphical software package designed for analyzing taxonomic and functional profiles. It provides statistical hypothesis tests and exploratory plots to identify significant differences between pairs or groups of profiles. The software supports various statistical tests, including Welch’s t-test, White’s non-parametric t-test, ANOVA, and Kruskal–Wallis H-test, and offers effect size measures and confidence intervals to assess the biological relevance of results. STAMP can process input data from multiple bioinformatic tools and generate publication-quality plots. The article demonstrates the use of STAMP on two microbial datasets: (1) taxonomic profiles from coalbed methane (CBM) communities and (2) functional profiles from photosynthetic and non-photosynthetic Cyanobacteria. The results highlight the distinct metabolic activities and taxonomic compositions of these microbial groups.STAMP (Statistical Analysis of Taxonomic and Functional Profiles) is a graphical software package designed for analyzing taxonomic and functional profiles. It provides statistical hypothesis tests and exploratory plots to identify significant differences between pairs or groups of profiles. The software supports various statistical tests, including Welch’s t-test, White’s non-parametric t-test, ANOVA, and Kruskal–Wallis H-test, and offers effect size measures and confidence intervals to assess the biological relevance of results. STAMP can process input data from multiple bioinformatic tools and generate publication-quality plots. The article demonstrates the use of STAMP on two microbial datasets: (1) taxonomic profiles from coalbed methane (CBM) communities and (2) functional profiles from photosynthetic and non-photosynthetic Cyanobacteria. The results highlight the distinct metabolic activities and taxonomic compositions of these microbial groups.