Is it permissible to kill flies in Makkah, whether one is in a state of ihram (ritual consecration) or not?

All perfect praise be to Allah, the Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad, sallallaahu ‘alayhi wa sallam, is His slave and messenger.

If flies are harmful and killing is the only way to get rid of them, then it is permissible to kill them. When one is in a state of ihram and he kills flies, he is not required to offer fidyah (expiation) or offer an equivalent of what he killed. Islam permits killing five types of harmful animals in the sacred precincts of Makkah. It was narrated that the Messenger of Allah, sallallaahu ‘alayhi wa sallam, said: "There are five (harmful) things upon whose killer there is no sin whether he is in a state of ihram or otherwise: rats, scorpions, crows, kites, and voracious dogs." [Muslim]

A person in a state of ihram is allowed to kill harmful animals, thus one is also allowed to do so when not in a state of ihram or outside of the sacred precincts of Makkah.

Allah Knows best.