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An in-depth study of the phylogenetic relationships of <i>Xylaria</i> species associated with nutshells of fruits and seeds within the genus <i>Xylaria</i> and related genera of Xylaceaecea was conducted in China. The multi-gene phylogenetic analyses were carried out based on ITS, RPB2, and TUB sequences of 100 species of 16 known genera in Xylariaceae around the world. Based on molecular phylogenetic analyses, morphological observations, and ecological habitats, a new genus, <i>Heteroxylaria</i>, is established to accommodate four new species, viz. <i>H. cordiicola</i>, <i>H. juglandicola</i>, <i>H. meliicola</i>, and <i>H. terminaliicola</i>, and four new combinations, viz. <i>H. oxyacanthae</i>, <i>H. palmicola</i>, <i>H. reevesiae</i>, and <i>H. rohrensis</i>. The genus is characterized by cylindrical stromata with conspicuous to inconspicuous perithecial mounds, surface black, having brown to dark brown ascospores with a germ slit, and it grows on nutshell of fruits. The combined ITS+RPB2+TUB sequence dataset of representative taxa in the Xylariaceae demonstrate that <i>Heteroxylaria</i> is grouped with <i>Hypocreodendron</i> but forms a monophyletic lineage. All novelties described herein are morphologically illustrated and compared to similar species and phylogeny is investigated to establish new genera and species.