Resident herbivorous damselfishes (Pisces: Pomacentridae) exclude other herbivores from their territories and reduce the grazing pressure within these territories. Among the damselfish, Stegastes nigricans is unique in that it manages a virtual monoculture dominated by the erect filamentous rhodophyte Womersleyella setacea, whereas many other herbivorous damselfishes maintain species-rich farms. We observed the behavior of S. nigricans in a lagoon in Okinawa, Japan, and discovered that this species intensively weeded out specific algae. To analyze weeding selectivity, we compared the algae picked up and discarded by S. nigricans to the algal assemblage found inside the territory. To examine the digestibility of each algal species, 10 damselfish were collected, and algae removed from their stomachs were compared with those found in the intestine and faeces. Inside their territories, S. nigricans selectively weeded out indigestible algae. These algae were late-colonizing Species, and the intensive weeding suppressed algal growth beyond early successional stages. Consequently, selective weeding enabled the fish to maintain virtual monocultural farms of a digestible early colonizer, W setacea, inside their territories.