A pregnant woman found dead next to her partner who was allegedly decapitated before his severed head was spiked on a stick has been identified.

Athena Georgopoulos, 39, was allegedly killed alongside her 50-year-old partner Andrew Gunn at their Mount Waverley home in Melbourne's south-east just before 10pm on Monday night.

Sinister graffiti was also found scrawled outside the Mount Waverley unit where the couple were allegedly murdered.

Heavily armed police swarmed the Adrienne Crescent property at 9.55pm on Monday after a neighbour heard yells and called triple-0.

Police allegedly discovered the man's mutilated body beside the dead a woman inside the unit in Melbourne's southeast but pair have yet to be formally identified.