Opposition leaders have sought to take advantage of splits within the ruling coalition in the run-up to the elections, in order to position themselves as serious challengers for the presidency.
Bongo, now in his seventies, came to power in 1967 as major oil finds were being made off Gabon's shores.
The country has enjoyed relative stability compared to other countries in the immediate region.
But oil output is declining and glaring social inequality and high unemployment have fuelled discontent.
Despite having a per capita income far above the African average and reserves of timber, manganese, gold, iron ore and uranium in addition to oil, half of the population still lives in poverty and the Gabonese complain of poor public services.
"It's the first time that I'm voting because they say there'll be transparency this time," 31-year-old Marianne Doumbou said as she voted.
"I'm voting so that my deputy can lobby the national assembly for us to have running water in our houses," she said, adding that public pumps were sited too far from many homes.
Soldiers and police stood guard as voting began peacefully at 2,525 polling stations around the country.
Bongo, who has been courting Chinese investment, has made clear he wants to secure a parliamentary majority to press ahead with his development plan for Gabon and its 1.4 million population.
Main opposition parties like the Gabon People's Union (UPG) party and the Gabonese Union for Democracy and Development (UGDD) have sought to turn discontent over the lack of basic resources into votes.
The leaders of these opposition parties - Pierre Mamboundou of the UPG and Zacharie Myboto of the UGDD - were defeated by Bongo in the November 2005 presidential election. They are now looking to boost their credibility as possible successors to him.