Bird's nest fungi involve six different genera, but only one of these genera (i.e. Cyathus ) have available mitochondrial genomes (mitogenomes) to date. In this study, we report the first mitogenome in the genus Nidula with Nidula shingbaensis K. Das & R.L. Zhao 2013 as a representative. The mitogenome is a circular molecule of 65,793 bp with a GC content of 26.2%. There are a total of 43 genes, including 14 typical protein-coding genes, 26 tRNA genes, two rRNA genes, and one free-standing intergenic open reading frame (ORF). Three introns (two in cox1 and one in cob ) are present in the mitogenome, with each containing an ORF encoding for a LAGLIDADG endonuclease. Phylogenetic analysis based on mitochondrial amino acid sequences confirms the phylogenetic placement of N. shingbaensis in Nidulariaceae in Agaricales. This study serves as a springboard for future investigation on fungal evolution in Nidulariaceae.