Zardari was arrested on arrival by air from Karachi after an anti-terrorism court there withdrew the bail granted to him earlier in connection with a 10 year old murder case of a judge and his son, which was one of the several criminal and corruption cases faced by him.
The Karachi court judge, Pir Ali Shah, while ordering the withdrawal of the bail also issued a non-bailable arrest warrant against Zardari, who was released on bail last month after spending eight years in prison.
Apparently he could not be arrested in Karachi as he had already boarded a plane to make his first visit to the capital after his release.
Before alighting from the plane, Zardari told TV networks over phone that the aircraft was held up for over two hours during which he learnt that his bail was withdrawn, a move described by him as a pressure tactic by the government to make his Pakistan Peoples Party (PPP) support it.
The plane was later allowed to travel to Islamabad where he was arrested after he alighted from it.
As Zardari got into police vehicle, he told his supporters to look after his children, local Geo TV reported, adding he also told his party workers not to worry and that he would be back soon.
Zardari is expected to be flown back to Karachi, Geo TV quoted officials as saying. Thousands of PPP workers, who had gathered outside the airport as well as in many other routes leading to airport, clashed with police.
Local television reports said police resorted to lathi charge and used water canons to disperse the crowds. The PPP has alleged that many of its leaders had been either prevented from going to the airport or detained.
Adding to the drama, the Sindh High Court has transferred Shah, the anti-terrorism court judge, from his post to the Sindh judiciary. The transfer was affected after the PPP lawyers approached the High Court, reports from Karachi said.
Zardari faced a host of civil and criminal cases instituted against him during the regime of former Prime Minister Nawaz Sharif, who himself was exiled to Jeddah after the military coup.
While Zardari languished in prison, Bhutto herself stayed abroad, mostly in Dubai and London to escape arrest in different cases registered against her along with Zardari.
Last month Zardari was released by the Supreme Court on bail. His release followed reports of an emerging rapprochement between Bhutto and President Pervez Musharraf.
PPP sources claimed the proposed deal, however, failed to materialise as the government wanted the party's blanket support for Musharraf's continuation as both the President and the Army Chief in lieu of his release, while Bhutto demanded safe passage for her return and holding of general elections.
During a recent visit to Karachi, Musharraf had ruled out mid-term polls and said elections would be held after the completion of the tenure of federal and legislative assemblies in 2007.