One of them, a Spaniard, on trial for charges of selling explosives to the men who carried out the bombings, dismissed suggestions on Wednesday that he worked with Basque separatist group Eta, describing such talk as "rumours".
Jose Emilio Suarez Trashorras, a former miner, told the court: "I don't have any relationship with Eta. These are rumours people have spread for their own ends," Trashorras told the court.
In another development, DNA testing has linked Abdelilah Hriz, a Moroccan man jailed in his homeland, to the bombings, a Spanish judicial source said on Wednesday.
The source said the Hriz, 29, was believed to belong to a "terrorist" organisation and to have been implicated in the March 11 attacks.
At the behest of Spanish investigators, DNA tests were done on Hriz last November and results linked him with samples found at two sites linked to the bombings of the four trains.
The samples were detected on a comb in a house where the bombs were believed to have been assembled and on trousers discovered in the apartment in the suburb of Leganes, where seven suspects blew themselves up during a police raid three weeks after the attacks.
Juan del Olmo, the examining magistrate, believes Hriz is a "material author" of the attacks and the trafficking of the explosives used to blow up the trains.
He also says Hriz was a member of a radical cell based in Madrid which carried out the attacks.
According to Del Olmo, Hriz had "direct and particularly intense links" with Mohamed Afalah, who fled Spain and is believed to have died in a suicide attack in Iraq, as well as Larbi Ben Sellam, now on trial in Madrid.
Del Olmo therefore ordered Hriz to be detained "pending national and international arrest warrants" being served on him.
It was not clear on what basis he was already in custody in Morocco.
The trial of 29 people accused of involvement in the blasts began on February 15 and verdicts are expected in October.