Reomel Ramones, 27, was led in handcuffs by National Bureau of Investigation (NBI) officers out of an apartment in the Pandacan district of the capital, Manila.
NBI chief Federico Opinion said Mr Ramones' 23-year-old girlfriend, Irene de Guzman, would present herself to authorities on Tuesday.
Criminal investigators seized a telephone, wiring and computer magazines but no computer from the couple's home, journalists were told.
The NBI said more arrests were likely.
The Love Bug virus, which created a flood of e-mails with the alluring subject line ILOVEYOU, is estimated to have caused several hundred million dollars of damage to computer systems worldwide.
Trail
FBI agents from the US were present during the raid at Mr Ramones' home on Monday.
The FBI and Interpol helped track the virus to the Philippines through an electronic trail left by the rogue e-mails but the investigation has thrown up several contradictory leads.
Police originally thought the main suspect was male, but said on Monday they were looking for a female computer school student from a middle-class family.
But the Philippines authorities are unsure if anyone can be prosecuted, because there is no specific law in the Philippines making the dissemination of computer viruses illegal.
The warrants for the search of the apartment were granted on the basis of a suspected breach of the banking laws.
Both Mr Ramones and Ms de Guzman are reported to be employees of a Philippines bank.
Clues
US security experts have said clues in the virus code point to a student at a computer college in the Philippines.
But some computer experts maintained that hackers elsewhere in the world could have got into the Philippines computer and used it to spread the Love Bug.
Swedish researcher Fredrik Bjoerck said traces on the internet pointed to a German exchange student living in Australia.
At least seven variations appeared soon after the virus began spreading, one masquerading as an e-mail joke, another as a receipt for a Mother's Day gift.
Anti-virus software maker Symantec said the latest variant of the virus poses as a warning message from their technical support team. Infected e-mails have the subject line Virus ALERT! and should be deleted.
E-mails infected with the Love Bug reached 45 million users, according to one estimate.
Estimates of the worldwide damage from the virus range from hundreds of millions of dollars to $10bn, mostly in lost work time.
Experts say the virus is likely to engender more variants in the coming weeks.
It only affects systems running Microsoft Windows with Windows Scripting Host enabled. Computers using Apple's operating system or Linux are not affected.