Madera Police identified him as 33-year-old Francisco Javier Bautista.
The Madera County Sheriff's Office said Bautista was wanted on several felony warrants.
They said he is known to posses firearms and has a violent criminal history.
Deputies say they served the search warrant at the home near Rotan Avenue and 4th street just after 4 p.m. on Friday.
For hours, they worked to get Bautista out of his home. They took him into custody just before 11 p.m.
He will be booked in on several felony charges of evading.
This is a separate incident from the standoff that took place in northeast Fresno, also on Thursday evening.
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The Madera County Sheriff's Office said 58-year-old Kirk Fitzgerald, an occupant of the residence in which Bautista barricaded himself, was arrested for being a felon in possession of a firearm.