Background: Function genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysis, differential epigenomic analysis or co-expression network analysis. While tools have been developed to identify biological functions that are enriched in the genes sets, there remains a need for comprehensive tools that identify functional enrichment of genes for both model and non-model species from a different function classification perspective. Results: We developed AllEnricher, a tool that calculates gene set function enrichment, with user-defined updatable libraries backing up for both model and non-model species as well as providing comprehensive functional interpretation from multiple dimensions, including GO, KEGG, Reactome, DO and DisGeNET. Conclusions: AllEnricher incorporates up to date information from different public resources and provides a comprehensive resolution for biologists to make sense out of specific gene sets, making it an advanced open-source tool for gene set function analysis.