The two men were identified as Jose Javier Oses Carrasco and Ugaitz Errazquin Telleria.
Oses is accused of belonging to ETA's urban arm, Kale Borroka, and Errazquin is accused of belonging to an ETA cell that killed businessman Inaki Uria and politician Isaias Carrasco.
Spain's Interior Ministry confirmed the arrests took place in Albi near Toulouse, but did not say when.
ETA declared an end to its armed struggle last October. However, Spain's Government has refused to negotiate with the group until it disbands. So far this year, 13 ETA suspects have been arrested.