We present a genome assembly from an individual Rugalucina vietnamica (Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1 089.88 megabases. Most of the assembly (99.85%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 30.68 kilobases. From the metagenome data, we recovered three bins, of which two were high-quality MAGs.