Authorities say they tracked two of them - Fabian Cruz Roman and Andres Nunez Rodriguez Jr. - to southern California on Tuesday night.
A third, Edgar Eduardo Ventura, was arrested a few hours earlier in the Firebaugh area in Fresno County.
Ventura, who is from Portland, Oregon, was facing charges of felony in possession of a firearm when he escaped. Merced County Sheriff Vern Warnke said at a press conference on Tuesday afternoon that he will face more charges due to the escape.
Roman and Rodriguez Jr. were caught in the San Diego area at about 8:30 pm.
Roman is currently in custody for murder charges and Rodriguez is in custody for attempted murder charges.
The hunt is on for the other three inmates, who are still on the run.
RELATED: Six inmates escape from Merced County Jail using homemade rope
Officials say on Saturday, the six men used a makeshift rope made out of sheets to escape from the building. Due to certain protocols that prohibit interrupting an inmate's sleep, authorities didn't notice the men were gone until the morning headcount nearly eight hours later.
The Merced County Sheriff's Office is working with several local, state, and federal law enforcement agencies, including the United States Marshalls Services, and the California Department of Corrections and Rehabilitation (CDCR) Special Services Unit, to track down the six inmates.
A tip line has been set up by the US Marshals Service and a reward of up to $5,000 per escapee is being offered for any information leading to their arrest.
To provide information you can call: 1-877-WANTED-2 (1-877-926-8332) or you can visit US Marshals website. All information given can remain anonymous and could help bring these criminals to justice.