One man in his 40s was held in Co Monaghan and the other, who is in his 30s, was picked up in neighbouring Co Louth.
Both were arrested under the terms of Irish anti-terrorist legislation that permits suspects to be kept in custody for up to 72 hours before being either charged or released.
They were being questioned at Carrickmacross, Co Monaghan. One man, Colm Murphy, of Co Louth, has so far been convicted in connection with the Omagh bomb attack by the Real IRA dissident terror group that killed 29 people and injured almost 300 others.
Three other men were held for questioning in connection with the blast by Irish detectives last week and subsequently released.
A spokesman said the latest arrests were part of an ongoing investigation into the bombing.