It happened at 12:45 p.m. when a taxi driver for East End Transportation was driving northbound on Wading River Road in Manorville.
MTAPD said the taxi with two occupants, drove around the crossing gates in the down position with lights flashing and bells sounding.
Police said the taxi appeared to have stopped on the tracks ahead of an approaching eastbound Long Island Rail Road train traveling from Ronkonkoma to Greenport, which struck the vehicle east of Yaphank Station, causing major damage to the vehicle.
Police said approximately 50 passengers were on board the double-decker diesel train and had no reported injuries on board.
The driver of the taxi was pronounced dead at Peconic Bay Hospital, police said.
The driver was identified as Daniel Seagren, 49, Ronkonkoma.
The taxi passenger was airlifted to Stony Brook Hospital in serious condition.
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