Nature photographer Joe Kelly was paddling up the Nissequogue River on a recent evening when he came upon a surprising sight: a pair of river otters lounging on a muddy bank.

Kelly grabbed his camera, capturing the latest evidence that the whiskered creatures are recolonizing Long Island.

"It was one of the coolest encounters in my whole life," said Kelly, 50, of Smithtown.

River otters largely vanished from the region more than 150 years ago, first because of hunting. Then came pollution and damage to waterways and marshes where they search for food.

Now, some naturalists say, the mammals are staging a comeback. Rarely seen for much of the last century, they have been spotted with increasing frequency in recent years.

Surveys of likely habitat and a rise in documented live sightings indicate a handful of river otters have indeed moved back and may be breeding.

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The otters have staked out territory in Oyster Bay and Cold Spring Harbor, in the tributaries of the Nissequogue River, and at East End sites stretching from Greenport to East Hampton, said Mike Bottini, an East Hampton biologist. In 2008, he documented almost 30 Long Island sites thought to be frequented by otters, based on tracks, tail drag marks and the fish scale-laden droppings they use to mark territory. More than half are near North Shore ponds, streams and marshes.

"That's their stronghold," Bottini said. "They're probably recolonizing Long Island by working their way along the Connecticut and Westchester shorelines." The quantity of tracks and droppings at a site near Mill Neck in 2008 suggested a breeding pair and offspring, he said.

At least 15 river otters have been documented on Long Island since the early 1990s, according to records from the state Department of Environmental Conservation and reports compiled from trappers, photographers and naturalists.

Live sightings such as Kelly's are rare. Secretive, nocturnal hunters whose home ranges can span 35 miles, river otters are tough to spot. Most of those documented here were snared in muskrat traps or, more commonly, ended up as roadkill.

"The first one I saw was on Route 347," said DEC regional wildlife manager Michelle Gibbons. "One of the roadkills we have mounted in our office."

The state does not track river otters on Long Island.

Biologist Eric Powers built three artificial otter dens to encourage breeding. Aided by an Eagle Scout, he placed the 3-foot-by-3-foot structures on private property near Caleb Smith State Park Preserve in Smithtown.

"If they were used I would be ecstatic," he said. "We're throwing out a welcome mat for the species to come back."