Larval habitats of the pest biting midge Culicoides ornatus were identified and characterised in a macrotidal mangrove creek system in Darwin Harbour in the wet-dry tropics of northern Australia. Sampling was undertaken during the mid to late dry season using submersible emergence traps to indicate larval activity. Substantial emergence was found in two well separated and distinctly different habitats: open creekbanks covered in Avicennia marina (Grey Mangrove) pneumatophores in the upper reaches of small tidal creeks and broad relatively flat areas dominated by Sonneratia alba (Mangrove Apple) at the mouth of the creek system. Intervening areas along creeklines were lined by Camptostemon schultzii (Kapok Mangrove) and did not support emergence activity. Adults emerging from each habitat were conspecific, based on comparison of mitochondrial COI gene sequences and a range of morphological characters. Nine different haplotypes were identified from 26 adults, with four haplotypes common to both habitats. Neighbour-joining analysis resolved all the haplotypes as a single highly supported clade with an average sequence difference of 1.6%. Features common to the two habitats included occurrence in sheltered mangrove-lined estuaries; occurrence in soft, fine, silt mud; presence of mangrove pneumatophores; and an open vegetation structure providing partial shade. Dense vegetation appeared to be a limiting factor. The tidal creek habitat was similar to C. ornatus habitats previously described from the east coast of Australia, but neither the Sonneratia zone nor other habitats at such a low tidal elevation have been previously associated with C. ornatus. This is the first detailed account of the larval biology of this important mangrove breeding pest species. The identification of likely C. ornatus breeding sites in Darwin Harbour and other similar ria coastlines of northern Australia should be possible from aerial photographs using the habitat descriptions presented in this paper.