Thraustochytrids, the exclusively marine organisms of kingdom Stramenopila and a source of essential fatty acids in the marine milieu, possess an osmoheterotrophic mode of nutrition and are therefore affected by type and source of available organic matter and pollution. To study their response to heavy metal pollution, they were isolated from the brown alga Sargassum cinereum from the coastal waters of Dona Paula, Goa, India. A total of 22 isolates were obtained from two samples collected during February and March 2012. Based on their 18S rRNA gene sequencing, the majority of the isolates were identified as Thraustochytrium kinnei. The rest were identified to be Sicyoidochytrium minutum, Ulkenia visurgensis and species of Thraustochytrium and Aurantiochytrium. Six isolates were screened for various enzymatic activities. Characteristic and distinctive enzyme profile was obtained from isolates of different genera. All isolates were also screened for their tolerance to heavy metals. They showed good growth in the presence of Mn2+. The other metals that were tolerated by most of the isolates were in the order Ni2+ > Cr6+ > Zn2+. Seven isolates grew in the presence of Cu2+, and six in the presence of Cd2+. The isolates growing on metals showed vast differences from their normal morphology such as small colony size, shrunken cells etc. Scanning electron micrographs revealed holes or depressions in the cell wall in the presence of metals. On the whole, the isolates belonging to Ulkenia visurgensis and Aurantiochytrium sp. showed tolerance to more metals than Thraustochytrium kinnei. Cluster analysis showed no peculiar trend of metal tolerance to any particular genus as the characters were scattered in the clusters.