The move was intended to cut waiting times.
Central Taxis and City Cabs, which between them have around 700 vehicles, were in talks about joining forces amid fears they were losing ground to the city's private hire trade.
Now, drivers from one of the firms appear to have scuppered the move following a meeting at Napier University's Craiglockhart campus.
Around 98 per cent of drivers with Central Taxis are understood to have voted to continue with the proposed merger, a move which would have seen a feasibility study carried out into the plans.
However, around 70 per cent of drivers with City Cabs, which is run as a co-operative, voted against it and the merger now appears to be dead.
The partnership is said to have been designed to counter the dual threat of the city's minicab trade and rival firm ComCabs, with the merged company able to provide a faster service to customers with its enlarged fleet.
Last year, the city's black cab firms described a decision by the city council to allow minicabs the right to charge lower fares as a "recipe for disaster".
The move raised objections from Central Taxis and City Cabs, who argued it would lead to "confusion" among passengers.
The city's biggest private hire firm, Edinburgh City Private Hire, won the right to change its meters and undercut its competitors by up to 30 per cent following the ruling by licensing chiefs.
A taxi trade source said: "The guys with Central were up for it, but the drivers with City Cabs voted two to one against it.
"Obviously they didn't consider it the right way forward. They were worried about being undercut by the private hire firms and the bosses thought a merged company would allow them to lower waiting times and pool their resources. It might also have allowed them to offer bigger discounts on client accounts."
Raymond Davidson, secretary of the Edinburgh Taxi Association, said mergers within the city's black cab companies still appeared to be "the way of the future".
He said: "I don't want to comment on the Central Taxis and City Cabs situation, but I would like to see the black cab firms merging together into a single company. In these difficult economic times, it makes sense for the companies to come together and share their strength to compete with the private hire firms."
No-one at Central Taxis or City Cabs was available for comment.