We present a genome assembly from a specimen of Montipora capitata (rice coral; Cnidaria; Anthozoa; Scleractinia; Acroporidae). The genome sequence has a total length of 689.31 megabases. Most of the assembly (99.26%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.87 kilobases. Gene annotation of this assembly by Ensembl identified 44 675 protein-coding genes.