We present a genome assembly of the diplonemid Rhynchopus euleeides (Euglenozoa; Diplonemea; Diplonemea; Diplonemidae). The genome sequence is 199.0 megabases long, with most of the assembly scaffolded into 88 chromosomal pseudomolecules. The multipartite mitochondrial genome and the 2.0 megabase genome of Ca. Syngnamydia salmonis, a bacterial endosymbiont of R. euleeides, were also sequenced and assembled.