Andrew Innes, 50, is alleged to have bludgeoned 25-year-old Bennylyn Burke to death with a hammer.
The software engineer is also alleged to have murdered her two-year-old daughter Jellica Burke by unknown means within his home during a 17-day window.
Innes faced a petition alleging two charges of murder when he appeared briefly in private at Dundee Sheriff Court.
App designer Innes is alleged to have carried out both murders within his home at 21 Troon Avenue between February 17 and March 5 this year.
The first charge alleges he attacked Bennylyn Burke by repeatedly striking her on the head with a hammer, or similar implement, and murdered her.
The second alleges he assaulted her toddler daughter "by means presently unknown to the prosecutor" and murdered her.
Innes appeared from custody, having been arrested at the weekend, and made no plea before Sheriff John Rafferty.
The case was continued for further examination and Innes was remanded in custody.
Meanwhile, a forensic team continued to search the detached home in Troon Avenue where a tent and skip have been stationed in the garden.
Officers arrived at the property on Friday afternoon and were in place throughout the weekend after initially responding to a missing persons inquiry.
Ms Burke and two children were last seen in Bristol on February 17 and were then reported missing from their home on March 1.
A seven-year-old girl was found alive in the Dundee property and is being supported by police.
It is understood Ms Burke originally hailed from the Philippines and travelled to live in Bristol around two years ago.
Police Scotland confirmed at the weekend that the investigation had become a murder inquiry although no bodies had been recovered at the time.
Ms Burke is understood to have had family members living in the United Kingdom and they have been informed as her next-of-kin.
One friend in Bristol paid tribute and told reporters: "This has broken our hearts and we are all constantly crying. It's just so sad.
"Jellica was so happy and such a sweet girl. Bennylyn was a full-time mum and her daughter was her life.
"She was a very bubbly girl and we always have a laugh together. She was very lovely and always smiling and so pretty. We are beyond devastated.
"Bennylyn was always just having fun with Jellica and we would meet up for pizza and picnics. The last time I saw them was in Bath before the lockdown came in December.
"She looked so happy. It's so heartbreaking thinking about it now."
Door-to-door inquiries have been carried out in the Ardler area of Dundee, where Innes lives in a £250,000 five bedroom house.
Officers are trying to establish the full extent of Ms Burke's movements in the period since she was last seen until Innes' arrest.
Detective Superintendent Graeme Mackie, of Police Scotland’s Major Investigation Team, said: "I would urge anyone with any information to please come forward and speak to us.
"This is a complex enquiry involving both local officers in Dundee and specialist resources from across Police Scotland.
"Bennylyn's next of kin have been updated on the arrest and are being supported by colleagues from Avon and Somerset Police.