Isbister played his first NHL game on October 1, 1997, for the Phoenix Coyotes (formerly the Winnipeg Jets) against the Chicago Blackhawks. His first NHL point was an assist, in a 3–2 Phoenix win over the Colorado Avalanche on October 11. He scored his first NHL goal ten days later on October 21, in a 4–3 loss to the Mighty Ducks of Anaheim. Isbister finished his rookie season with 17 points in 66 games. After his second season with the Coyotes, Isbister was traded to the New York Islanders on March 20, 1999, with a third round draft choice (Brian Collins) in 1999 for Robert Reichel, a third round draft choice (Jason Jaspers) in 1999 and a fourth round draft choice (previously acquired from Ottawa; Phoenix selected Preston Mizzi) in 1999.