Thraustochytrids are ubiquitous, chemo-organotrophic, marine stramenipilan protists belonging to the class Labyrinthulomycetes. Their taxonomy is largely based on life cycle development stages. We describe here a new species of thraustochytrid isolated from mangroves of Goa, India. The organism is characterized by large zoosporangia with two distinct development cycles. In one, typical thalli with ectoplasmic net elements mature into zoosporangia that divide to form heterokont biflagellate zoospores, leaving behind a proliferation body. In the second type, the thalli develop into amoeboid cells, reminiscent of the genus Ulkenia Gaertner. Unlike Ulkenia, however, the 'amoebae' do not immediately produce zoospores, but round up prior to division into zoospores. The two types of development occur simultaneously in single cell-derived in- vitro cultures. Molecular characterization of the new isolate involving 18S rRNA gene typing and comparative phylogenetic analysis further establish it to be a new and distinct thraustochytrid species with Schizochytrium aggregatum Goldstein and Belsky and Thraustochytrium kinnei Gaertner as the closest forms. We have named this new species as Thraustochytrium gaertnerium, deriving its species name in honour of Dr Alwin Gaertner, a pioneer in the studies of taxonomy and ecology of thraustochytrids.