Microdiamonds in metamorphic rocks are a signature of ultrahigh-pressure (UHP) metamorphism that occurs mostly at continental collision zones. Most UHP minerals, except coesite and microdiamond, have been partially or completely retrogressed during exhumation; therefore, the discovery of coesite and microdiamond is crucial to identify UHP metamorphism and to understand the tectonic history of metamorphic rocks. Microdiamonds typically occur as inclusions in minerals such as garnet. Here we report the discovery of microdiamond aggregates in the matrix of a metapelite from the Nishisonogi unit, Nagasaki Metamorphic Complex, western Kyushu, Japan. The Nishisonogi unit represents a Cretaceous subduction complex which has been considered as an epidote–blueschist subfacies metamorphic unit, and the metapelite is a member of a serpentinite mélange in the Nishisonogi unit. The temperature condition for the Nishisonogi unit is 450 °C, based on the Raman micro-spectroscopy of graphite. The coexistence of microdiamond and Mg-carbonates suggests the precipitation of microdiamond from C–O–H fluid under pressures higher than 2.8 GPa. This is the first report of metamorphic microdiamond from Japan, which reveals the hidden UHP history of the Nishisonogi unit. The tectonic evolution of Kyushu in the Japanese Archipelago should be reconsidered based on this finding.