"We must demand the end of terrorism by being united," one of the organisers of the Madrid march, a group representing Ecuadorian associations in Spain, repeatedly said, in vain, this week.
It wants to pay tribute to the two Ecuadorians who were killed in the December 30 attack at Madrid airport, which also dashed hopes of peace talks between the government and Eta to end decades of violence.
The bombing was the first deadly attack by Eta since May 2003 and broke their nine-month unilateral ceasefire. Although Eta, which claimed responsibility, has maintained its ceasefire still holds, this is rejected by the government.
For years Eta had waged a bloody struggle for an independent homeland for Basques in parts of northern Spain and southern France.
Two notable political heavyweight absentees from Saturday's rallies were the main conservative opposition Popular Party (PP) and Eta's political wing, Batasuna, banned in 2003 by the Spanish judiciary.
The PP said it would not attend the rally planned for Madrid as its slogan "for peace, life and against terrorism" did not include a clear call "to defeat Eta". Despite a change to the slogan by organisers, it still failed to satisfy.
The powerful pro-PP Association of the Victims of Terrorism also shunned the marches.
And in Bilbao, Batasuna was missing, despite having originally said it would take part. It announced its U-turn late on Friday after the regional Basque presidency urged the Bilbao rally to call on Eta to renounce violence.
Batasuna had considered that the initial slogan "for peace and dialogue" was sufficient to attend, but drew the line at the call for a renunciation of Eta violence.
The divisions reflect the difficulties facing the socialist government of Jose Luis Rodriguez Zapatero, the Spanish prime minister, in forging a united political front on the fight against terrorism since the Madrid attack.