Precise identification of fungi is crucial in scientific communication, but commonly used methods such as BLAST are prone to misidentifications. To address this challenge, we have developed FunID, a phylogenetic tree-based fungal identification pipeline (https://github.com/Changwanseo/FunID). FunID utilizes an end-to-end phylogenetic tree-based approach with multi-genetic marker data and incorporates algorithms for detecting and filtering out errors. It is designed to be user-friendly, allowing researchers to easily construct and distribute database, assign higher taxa, select appropriate outgroups, and interpret and visualize trees. FunID can also detect errors, including human and database errors, such as misspellings, incorrect gene assignments, and misidentified sequences. Further, we evaluated the performance of FunID with three datasets with diverse taxa, taxonomic level, and number of genetic markers to assess its universal effectiveness in fungal identification. We believe that FunID can prevent misidentifications and significantly enhance the fungal species identification.