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Brothers Arlo (11) and Philip (12) Ruston-Wood were swimming near Portobello last Wednesday when what they think was a large stingray, swam past them.
''We decided we would go swimming and Arlo went first and I was wading out and crouched down then I just saw this thing coming towards me and then I shouted, 'Arlo it's a shark','' Philip said.
Arlo, who was wearing goggles, said he was underwater when through a large cloud of mud he saw two large eyes and wings swim past him about an arm's length away.
''We quickly ran out of the water because it was only knee-deep. It was kind of slow for me though because I had my flippers on,'' he said.
Both boys had seen rays before, but never in Otago Harbour.
Despite their close encounter they both went swimming later that day in the same area - but on reflection might avoid it for a while.
Portobello laboratory manager Doug Mackie said rays were not uncommon in the harbour. He had seen one about two years ago from his office window.
''I'm not a particularly observant person so if I have seen one then other people would have too.''
Divers often reported seeing rays and liked to compare notes to determine who had seen the largest one, Dr Mackie said.
''They can be quite large and impressive when you see them up close,'' he said.