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<i>Coolia</i> is a genus of marine benthic dinoflagellates which is widely distributed in tropical and temperate zones. Toxicity has been reported in selected <i>Coolia</i> species, although the identity of causative compounds is still controversial. In this study, we investigated the taxonomical and toxicological aspects of <i>Coolia</i> species from Brazil. Since light- and electron microscopy-based morphology was not enough to distinguish small-celled species, ITS and LSU D1-D3 phylogenetic analyses were used for species definition. Cultures of <i>Coolia palmyrensis</i> and <i>Coolia santacroce</i> were established from samples collected along the northeastern Brazilian coast, the first record of both species in South Atlantic waters. Cultures of <i>Coolia malayensis</i> and <i>Coolia tropicalis</i> were also established and exhibited acute <i>in vivo</i> toxicity to adults of <i>Artemia salina</i>, while <i>C. palmyrensis</i> and <i>C. santacroce</i> were non-toxic. The presence of 30 yessotoxin analogues, 7 metabolites of <i>Coolia</i> and 44 <i>Gambierdiscus</i> metabolites was screened in 14 strains of <i>Coolia</i>. 44-methyl gambierone (formerly referred to as MTX3) and a new isomer of this compound were detected only in <i>C. tropicalis</i>, using both low- and high-resolution LC-MS/MS. To our knowledge, this is the first report of gambierone analogues in dinoflagellates other than <i>Gambierdiscus</i>; the role of <i>C. tropicalis</i> in ciguatera poisoning thus deserves to be considered in further investigations.