Asexual reproduction is by binary cell division, during which the parental flagellum is resorbed and the flagella of the two daughter cells appear:
Flagellar replication: early stage in cell division
One daughter cell typically remains in the parent theca while the other swims away as a zoospore.
Cysts are not yet known for Monosiga, though they have been described for species in other choanoflagellate genera. Sexual reproduction is unknown.