One of the men was reportedly the son of the couple, both in their 60s.
Neither he or the other man charged entered a plea when they appeared in court on Monday, local media say.
The couple’s older son reported them missing on 9 March. Police are still searching for their missing body parts, with some found at an apartment.
The son, 29, and the other man, 35, were charged with two counts of murder on Sunday, police say.
The younger son had told police the couple were on their way to China, but suspicions were raised when no records of them leaving were found, the South China Morning Post reported.
“The investigation continues on the motive of the case,” a police spokeswoman was quoted by Agence-France Presse news agency as saying.
They believe the couple’s other body parts have been disposed of into the sea near the apartment, but divers have been unable to retrieve any so far.
Two other murders also shook Hong Kong over the weekend.
A teenager is accused of stabbing his father to death and wounding his mother in a dispute about video games.
A woman also jumped from a building after allegedly killing her partner