The Marlins lost 5-2 to the Padres on Friday night, taking back-to-back losses to open the series with the Friars.
The loss drops the Marlins to 41-57 and a season low 16 games under .500.
The Padres got out in front in the first inning, thanks to a Tommy Pham home run to right-center, just the second allowed by Thompson this season. Jake Cronenworth would follow immediately after with a triple, then come across to score on an RBI groundout by Manny Machado. The Marlins were down 2-0 before they could blink.
Thompson got two quick outs in the second inning, but let up a double to Padres starting pitcher Joe Musgrove.