Munoz had an 8-under 64 at the Ko Olina Golf Club course to finish 36 holes at 136. Ai Miyazato was also tied for the lead after shooting a 65.
After high winds made scoring difficult on the opening day of the event, several low scores were recorded Thursday.
Jimin Kang was alone in third at 138 after shooting a 66 while those tied for fifth at 139 included Meena Lee, Suzann Pettersen and Brittany Lang. Lee had a 65 to battle her way into the tournament after struggling to a 74 Wednesday.
Michelle Wie did not come close to making the cut, finishing 36 holes 18 shots out of the lead.
Swim Week Miami Beach 2014 [PHOTOS]