We present a genome assembly of Myriophyllum alterniflorum (Alternate Water-milfoil; Streptophyta; Magnoliopsida; Saxifragales; Haloragaceae). The genome sequence has a total length of 244.22 megabases. Most of the assembly (93.29%) is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial sequence has a length of 436.55 kilobases and the plastid genome assembly has a length of 158.64 kilobases. Gene annotation of this assembly on Ensembl identified 19 107 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.