These are actually 2 separate periods. Jean takes up the green Phoenix costume in the late 90s while she and Scott are still together, but after he "dies" (merges with Apocalypse) at the end of "The Twelve" storyline the entire team then changes costumes, including Jean. She went through a few costume changes.
Years later, mid 2000s I believe, Morrison had Jean actually acquire the Phoenix powers herself during his run, seemingly for the 1st time since it was retconned that the original Phoenix replaced Jean, it wasn't Jean. It's at this point that Jean herself IS the Phoenix, but she wore the standard black X gear of the time, not the traditional Phoenix costume, up until her last issue or two, then changed to the traditional green Phoenix costume, but maybe 2 issues later Xorn/Magneto killed her, she's been dead since except for the Phoenix Endsong books.
Dear God I'm a nerd.