According to a report by BBC News, Ona was honoured for his fight to stop what he describes as a destructive mining project in the Ivindo National Park.
He is one of seven people from six continental regions to be awarded an equal share of the 900,000 dollars (600,000 pounds) 2009 Goldman Environmental Prize.
It has been described as "the Nobel Prize for grassroots environmentalism".
Ona has campaigned for three years against the Belinga mine project - a deal between the government in Gabon and the Chinese mining and engineering company, CMEC, to extract iron ore.
The project includes the construction of a large hydroelectric dam, which is already underway, to provide power for the mine.
The dam is being built on the Ivindo River, near the Kongou Falls, Gabon's highest waterfall.
Ona, who described the falls as "the most beautiful in central Africa", said that Gabon's government had failed to consult the local population and had not assessed the impact of the development on the environment before it gave permission for construction to begin.
Ona and his colleagues embarked on their campaign, working with other environmental NGOs, holding news conferences and meeting with local communities.
There has been no construction in Ivindo for almost a year, but Ona says this has more to do with the economic crisis and the price of iron ore than with the Gabonese government backing down.
He told BBC News that he hoped his receipt of the Goldman Prize would "draw international attention to just how precious this area is".
"Some of the money from this award will go to the functioning of Brainforest, and the rest will be allocated to setting up small- and medium-sized businesses for local communities," he said.
"I want to set up a clinic near Ivindo where the local people can be treated using traditional medicine. Some of the money will serve to establish this health centre for all of those communities," he added.