It's believed the human remains found at Cape Schanck on the Mornington Peninsula on Monday belong to Maryam Hamka, police say.
The 36-year-old was reported missing by her family on April 15, 2021.
She was last seen leaving a Brunswick Woolworths at 5.30pm on April 10.
Police have charged two men over Ms Hamka's alleged murder.
Her boyfriend Toby Loughnane will stand trial in the Supreme Court.
Oscar Newman also faces trial charged with assisting Loughnane to avoid apprehension.
Police said they hoped the discovery would provide some relief for Ms Hamka's relatives and friends.
"The investigation has been an arduous and long one over the last couple of years and the efforts of the missing person squad has resulted in the finding of the remains earlier today," Detective Inspector David Dunstan told reporters on Monday.
"Our heartfelt thoughts are with Maryam's family and friends. The past two years have been incredibly difficult for them.
"We know this has been an incredibly difficult time for Maryam's family and traumatic and we hope this will bring some closure to finally let Maryam rest in peace."
Police previously searched the Cape Schanck area last month and returned on Monday.
The remains were found about 10.30am in bushland off Rogers Road near Patterson Road.
They will be sent to the coroner for formal identification and a post-mortem examination.
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