Federal police in Tijuana said they arrested about a dozen members of the Jalisco New Generation Cartel who claimed to be in charge of the tunnel.
This organization was thought to be anchored in the state of Jalisco and in other parts in Central Mexico, but not this far north along the border.
Some people south of the border said it's troubling because the Jalisco cartel has been described as "ultra violent" and "hyper ruthless."
There's worry another clash between cartels will erupt as they start fighting for control of the valuable Tijuana-San Diego drug route.
"They started out as an enforcer group, then gradually became autonomous taking over routes and smuggling operations," said Scott Stewart, vice president for Stratfor Tactical Analysis, a geopolitical intelligence and advisory firm based in Austin, Texas.
Stewart told FOX 5 they've been tracking the Jalisco cartel for quite some time and have seen an "uptick in violence in Tijuana."
Federal police in Tijuana confirm this and attribute the increased bloodshed on the newcomers as they try to establish themselves against their bitter rival, the Sinaloa cartel, operated by Chapo Guzman.
They fear more bloodshed will take place in the coming months along the border.