Based on our widely used web-based application WebGestalt, we developed a new R package WebGestaltR that blends the strenths of web- and R-based enrichment analysis tools. WebGestaltR supports flexible input data types for the local and batch analysis, directly accesses 324 gene identifier and 150,937 functional categories from the WebGestalt server, performs the Over-Representation Analysis or Gene Set Enrichment Analysis and outputs an interactive html report.