Molina, 20, clocked 2:16.88 to beat Thai Vorrawuit Aumpiwan (2:17.56) and Indon Herry Yudhianto (2:21.92) for his third gold medal following his triumphs in the 400-m and 200-m individual medley as the Philippines surpassed its performance in the last SEAG in Vietnam.
Miguel Mendoza followed up Molinas victory with a golden swim in the 1,500-m freestyle even as RP captured three silver medals and one bronze in a productive day to the delight of the big crowd at the P60-million state-of-the-art venue.
"This sparks the Philippine bid to power itself forward to the overall championship," said swimming president Mark Joseph.
Mendoza, a University of Georgia 22-year-old tanker, submitted a 15:47.36 clocking to successfully defend his title and at the same time break the RP mark of 15:49.55 he established in Hanoi.
Molina, a fourth year International Relations student at University of California in Berkeley, also registered a new national record of 2:19.19 he set in the World Championships in Montreal, Canada early this year.
And as he received his gold medal, Molina wrapped himself up with the Philippine flag and sang the National Anthem almost in tears.
Gerard Gabriel Grabador, who was swimming third in the first two turns, finished sixth in 2:23.95.
Molina goes for a fourth gold in the 200-m freestyle, and possibly, another one as he teams up with Grabador, Timmy Chua and Filipino-American James Walsh in the 400-m medley relay in todays fifth and final day of pool competition offering six gold medals.
Mendozas triumph proved to be more dramatic.
After trailing Thai Charnvudth Saengsri by a full body length, Mendoza unleashed a monster of a rally in the final 200 meters to beat the Hanoi silver medallist and seal the win that sent the crowd into a frenzied mood.
Saengsri settled for silver in 15:55.42 while another local bet, University of the Philippines Ryan Arabejo, fought his way back from fourth place to third to snatch the bronze in 16:09.88.
Presidential son Datu Arroyo awarded the gold medal to Mendoza under scattered rains as the National Anthem was played for the second time.