A collection of submerged wood samples in the Pyrénées, France, led to the discovery of a new freshwater Dothideomycetes genus. Amniculicola lignicola gen sp. nov, is described and illustrated. In addition, rDNA and RPB2 gene sequences are analysed phylogenetically to investigate its ordinal and familial placement. Morphologically, Amniculicola resembles species of Ostropella and Xenolophium in having subglobose ascomata with prominent lips surrounding a slit-like ostiole. However, it is readily distinguished from Ostropella and Xenolophium by ascus shape and in having a short pedicle and thin peridium. Phylogenetic analyses based on 28S rDNA sequences also indicated that A. lignicola and O. albocincta (type species of Ostropella) are phylogenetically distinct. Morphological characters indicate that Amniculicola belongs in the Pleosporales and this is supported by molecular data. Sequences analyses from three loci suggest that it is closely related to anamorphic fungi, such as Anguillospora longissima, Spirosphaera cupreorufescens, and Repetophragma ontariense; however, its affinities with known Dothideomycetes and its familial placement are still unresolved.