Blayze James Noble, 33, appeared in Alice Springs Local Court on Monday charged with killing Christine Joyce Dianne Marshall Hunter, 27.
She was found dead with "visible facial injuries" in a Jeep Cherokee beside the Barkly Highway near the Northern Territory's Tennant Creek on April 5.
The Sunshine Coast pair had been on a cross-country trip from Queensland when Noble rang emergency services about 5.50am, police said.
He allegedly said the woman was not breathing after their car hit a kangaroo on the highway near Barkly Homestead.
NT Police Acting Commander Mark Grieve said information obtained at the time led officers to believe Ms Hunter had been assaulted by the man earlier that morning.
Police released a photo of the Jeep which showed damage to the front.
Mr Grieve told reporters investigators were trying to determine whether the damage was "pre-existing or whether it was fresh".
"At this point in time, we haven't been able to locate any evidence of that particular (kangaroo) strike occurring," he said.
An autopsy was under way to determine a cause of death.
The couple's movements leading up to Ms Hunter's death were traced by NT Police working with their Queensland counterparts.
They are believed to have been on a trip since April 1, driving from Gympie in Queensland through to the NT's Barkly Homestead over four days.
Judge Anthony Hopkins on Monday remanded Noble in custody and adjourned the matter until July 30 for a preliminary examination mention.
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