A molecular taxonomic study on the north European species of the genus Agathomyia Verrall (Diptera: Platypezidae) is presented. We include molecular phylogenetic analyses based on two fragments of the mtDNA COI and a fragment of the nuclear 28S rDNA genes for both adult and immature stages of Agathomyia spp. The Agathomyia elegantula (Zetterstedt) group taxa were revised based on the newly obtained molecular and morphological data. Two new species belonging to the A. elegantula group were described, Agathomyia alneti St ahls & R€ attel sp.n. and A. shatalkini St ahls sp.n. Agathomyia boreella (Zetterstedt) and A. scutellaris (Zetterstedt) were resurrected from synonymy of A. elegantula Zetterstedt. The genus Antrodiella Ryvarden & I.Johans was recorded as fungal host for Agathomyia elegantula group species and is a new host fungus genus for Platypezidae and for genus Agathomyia. Antrodiella faginea and A. pallescens were recorded as host fungi for A. boreella, A. pallescens for A. elegantula and A. serpula for A. alneti sp.n. We present identification keys to males and to all hitherto known third-stage larvae of north European Agathomyia species including digital images, and discuss conservation aspects for these taxa.