The bodies were found dumped by a roadside near the city of Monterrey in northern Nuevo Leon state.
An army spokesman said Daniel Jesus Elizondo, known as El Loco, or The Madman, was arrested by troops.
The authorities say he is the local leader of the Zetas drug cartel, which, they say, left threatening messages with the bodies.
In a statement, Mexico's defence secretary said Mr Elizondo was detained on 18 May in Cadereyta municipality, where the 49 bodies had been found six days earlier.
However, information about the arrest was only made public on 20 May.
Security officials said the 43 men and six women had been decapitated and had their hands cut off, making identification difficult.
Cadereyta is on the road from Monterrey to Reynosa on the US border.
Mexican authorities blamed the killings on a conflict between rival drugs gangs - a note left with the bodies said they had been killed by the Zetas cartel.
It is the latest in a series of recent massacres in northern Mexico.
The Zetas have been fighting the Gulf and Sinaloa cartels for control of smuggling routes into the US.
Security officials said the bodies, some of which were in plastic bags, appeared to have been killed at another location up to two days ago and dumped from a truck.
Nuevo Leon's prosecutor, Adrian de la Garza, said the fact that hands and heads had been cut off made it difficult to identify the victims, but he said it was possible they were Central American migrants.
Around 50,000 people have died in drug-related violence in Mexico since December 2006, when President Felipe Calderon deployed the army to combat the cartels.
The three main candidates to succeed Mr Calderon in July's presidential election have all said they would work to end the violence, but have not offered any concrete plans.
Source: BBC News
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