This is the first report of planktonic choanoflagellates from the Chilean coast, relating their abundance with that of bacteria and viruses. Surface water samples were taken off Antofagasta, Montemar, and Puerto Montt and samples from ballast tanks were also analyzed. The choanoflagellates were identified following morphological type descriptions. Viruses and bacteria were stained with SYBR Green and choanoflagellates, bacteria, and viruses were counted simultaneously using red autofluorescence for the former and green fluorescence for the latter two. Six species of Acanthoecidae were observed for the first time in Chilean waters: Calliacantha multispina (0.3-10³ L-1), Acanthocorbis apoda, Stepha-noeca diplocostata (2.0-10³ L-1), Crinolina isefiordensis, Parvicorbicula superpositus, and Pleurasiga minima (5.0-10³ L-1). The concentrations of bacteria (1.1-10(6)-4.5-10 6) and viral-like particles (VLPs) (7.9-10 6-21-10(6)) agreed with those typically found in marine coastal waters. In addition, Acanthocorbis asymmetrica was found in ballast waters, where its high concentration (20-10³ L-1) likely resulted from the particular physical and biological environment therein