PowerMarker is an integrated analysis environment (IAE) for genetic marker analysis, offering a user-friendly graphical interface for data management, analysis, and visualization. It supports over 50 statistical analyses for genetic markers, including Hardy-Weinberg equilibrium tests, linkage equilibrium tests, and linkage disequilibrium (LD) analysis. PowerMarker handles various marker data types, including haplotypes and diplotypes, and supports multiple input formats, including table-like formats. It can export datasets in various formats and provides tools for population differentiation using F-statistics, marker selection, and phylogenetic analysis. The software also includes methods for testing associations between markers and traits, including case-control tests and haplotype trend regression. PowerMarker is implemented in Visual C# and runs under the Microsoft .NET framework, with Excel integration and multithreading support for efficient data processing. It does not currently support linkage analysis but plans to add this in future versions. The software is continuously updated to support new analyses and is supported by NSF grants. PowerMarker provides special features such as 2D plots, triangle plots, and Excel integration for data visualization and analysis. It is designed to reduce data preparation time and ensure data integrity throughout the analysis process.PowerMarker is an integrated analysis environment (IAE) for genetic marker analysis, offering a user-friendly graphical interface for data management, analysis, and visualization. It supports over 50 statistical analyses for genetic markers, including Hardy-Weinberg equilibrium tests, linkage equilibrium tests, and linkage disequilibrium (LD) analysis. PowerMarker handles various marker data types, including haplotypes and diplotypes, and supports multiple input formats, including table-like formats. It can export datasets in various formats and provides tools for population differentiation using F-statistics, marker selection, and phylogenetic analysis. The software also includes methods for testing associations between markers and traits, including case-control tests and haplotype trend regression. PowerMarker is implemented in Visual C# and runs under the Microsoft .NET framework, with Excel integration and multithreading support for efficient data processing. It does not currently support linkage analysis but plans to add this in future versions. The software is continuously updated to support new analyses and is supported by NSF grants. PowerMarker provides special features such as 2D plots, triangle plots, and Excel integration for data visualization and analysis. It is designed to reduce data preparation time and ensure data integrity throughout the analysis process.