Myconymphaea yatsukahoi is a fungus that has only been isolated once from a forest in the Sugadaira Research Station, Nagano, Japan. Over 20 y have passed since its first discovery but since then it has not been rediscovered. Here, we re-isolated M. yatsukahoi from the type locality and another location, Tambara Moor, Gunma, Japan. Sporophores of this species were detected by direct field observation in Sugadaira and by induction from soil from Tambara. We attempted to narrow down isolation sources of this species by investigating the excrements of Lithobiomorpha and Scolopendromorpha centipedes, which are frequently found in the two locations where the species is distributed. In both locations, we found M. yatsukahoi in the excrements of Lithobiomorpha but not Scolopendromorpha. Myconymphaea yatsukahoi appears to be a coprophilous fungus and the excrements of the predators living in soil may be promising isolation sources for understanding the hidden diversity of kickxellalean fungi.