But its main rival, the National Rally for Democracy, which is backed by the powerful DRS intelligence service, came second and the two rivals are squaring off for crucial presidential elections scheduled for 2014.
The Islamists, who ran in the May 10 poll for the first time in two decades, were too disorganized and fractious to make much of an impact despite massive gains made by other Islamist parties in the aftermath of the Arab Spring pro-democracy uprising across the Arab world in 2011.
The poor voter turnout -- around 58 percent of the electorate abstained -- was most apparent in the cities and underlined the chronic apathy that has gripped the oil-rich, corruption-riddled North African state, which has been ruled by the FLN and the generals since independence.
This was particularly evident among the disillusioned younger generation.
It's battling high unemployment, the unequal distribution of energy revenues and what the hammerlock on power held by the generals and their political allies, collectively known simply as "le pouvoir" -- the Power.
The FLN secured 220 of the 462 parliamentary seats, nearly doubling its representation, largely because the independence war generation turned out in significant numbers to vote.
The smaller NRD, led by Prime Minister Ahmed Ouyahia, a Berber like many other senior officials in the DRS, took 68 seats. The Green Alliance, a moderate Islamist bloc, secured 42 -- 12 percent -- of the seats, well below expectations and a fraction of the FLN's 62 percent.
Algeria has largely avoided the bloody political convulsions that swept four longtime Arab dictators from power in 2011. But that's mainly because President Abdelaziz Bouteflika, who's ruled since 1999, contained the domestic impact of the uprisings through tough security, hefty public spending increases -- including a $25 billion increase in public sector salaries, thanks to energy revenues -- and some reforms.
The poor turnout was seen as a serious setback for "le pouvoir" and underlined that popular resentment remains a threat.
"Violence may increase due to persistent levels of discontent and other systemic problems, but it is unlikely to reach the level of a wide-scale uprising that threatens the current regime's hold on power," Oxford Analytica observed.
One reason for this is that Algeria's 36 million population still recoils in horror at the savagery of the 1992-2002 civil war triggered when the military scrapped a general election the Islamists were set to win.
Some 200,000 people were killed, many of them in horrifying massacres carried out by the Islamists and the security forces.
Bouteflika is credited with ending the bloodshed through a reconciliation program when he was first elected. The bloodletting left the Islamists divided and weak.
However, the low turnout demonstrated "the majority in large urban centers doesn't believe in change through politics," cautioned Geoff Porter of North Africa Risk Consulting Inc.
The election "gives the army considerable influence in a Parliament expected to draft a new constitution," global security consultancy Stratfor noted.
"The electorate may still reject any attempt by the army at power consolidation that excludes minority parties during the drafting of the constitution."
But the most dangerous element in Algerian politics is the power struggle between the army and the intelligence apparatus led by the DRS.
This reflects the ethnic fault line that runs through Algerian society, the conflict between the ruling Arabs of the coastal cities and the largely dispossessed Berbers who make up roughly a quarter of population.
The military is dominated by Arabs, while the DRS is heavily under Berber influence.
Although it doesn't have its own party, like the military has the FLN, the DRS, through its Berber chief, Mohamed Mediene, has close links to Interior Minister Dahou Ould Kablia, Energy Minister Youcef Yousi and Ouyahia, the NRD leader -- all Berbers.
Bouteflika, serving his third term and in failing health, seeks to pass the baton to his brother Said, against the wishes of the DRS which has turned on him and is expected to put up its own candidate for the presidency.
"In the short term," observed Stratfor, "the biggest threat to Algeria's political stability is the quiet, ongoing competition between the military and the intelligence services."
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