Although the dwarf minke whale is known only from the southern hemisphere, it seems more closely related to the northern hemisphere minke whale, Balaenoptera acutorostrata, than to the Antarctic minke whale, Balaenoptera bonaerensis. It is currently regarded as an un-named subspecies of B. acutorostrata, but may be a distinct species. Both Antarctic and dwarf minke whales are found in GBR waters but only one Antarctic minke has been observed over the continental shelf in the northern region. The two species can be distinguished by their size and colouration: (1) female dwarf minkes have a maximum size of about 7.8 m, on average about 2 m shorter than Antarctic minkes, and (2) dwarf minkes have a white shoulder blaze and flipper base, with a dark grey tip on the flipper, in contrast to Antarctic minkes that have a light to dark grey shoulder and a uniformly paler grey flipper.
In the GBR region, dwarf minkes have been recorded from north of Cape Grenville Island to the Swain reefs. This distribution may reflect the pattern of human use of the region rather than the actual distribution of the whales. Dwarf minke whales are seen in the northern GBR between March and November, with over 90% of sightings in June and July. The outer shelf region from Ribbon Reef 10 (near Lizard Island) south along the Ribbon Reefs to Agincourt Reef is the main focus for minke whale tourism. People are allowed to swim with minke whales from permitted vessels in the Great Barrier Reef Marine Park, but only if the whales initiate the encounter. Regulations govern people's behaviour during such encounters. The colour patterns of dwarf minke whales are the most complex of any baleen whale and are used to identify individuals by researchers, with particular whales being sighted repeatedly over periods of up to eight years.
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