We present a genome assembly of the diplonemid Diplonema japonicum YPF1604 (Discoba; Euglenozoa; Diplonemea; Diplonemidae). The genome sequence is 62.30 megabases in span. Most of the assembly is scaffolded into 118 chromosomal pseudomolecules. The multipartite mitochondrial genome was also assembled. The genome sequences of two bacterial endosymbionts, Ca. Cytomitobacter primus and Ca. Cytomitobacter primus, were also assembled.