HaploGrep is implemented as a web application based on Phylotree, a periodically updated classification tree estimated from data worldwide. Any given range of the mitochondrial genome can be used for haplogroup classification, which is based on the phylogenetic stability of mtDNA polymorphisms. For every input sample the top ten results and the phylogenetic position of the respective haplogroup are displayed, thus providing a detailed explanation how and why a haplogroup was ranked best. HaploGrep generates an interactive data visualization of the results and provides recommendations which polymorphisms should be analyzed additionally to get a more accurate result. HaploGrep is free and can be used without any login.