The moves came two days after Marlins owner Jeffrey Loria fired President of Baseball Operations Larry Beinfest and special assistant Jim Fleming.
The Marlins have struggled to a 61-100 record coming into Sunday's final game of the season. They have gone 130-193 since moving into their new downtown Miami stadium last year.
Hill, who has been with the Marlins for 11 seasons, has been the team's GM since 2007, while Jennings had been the vice president of player development and assistant general manager.
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