The Foton-M4 satellite returned to Earth on Monday, the Roscosmos agency said in a statement (in Russian).
Experts say the geckos may have frozen to death after the heating system broke down, Russian news agencies report.
They were sent into space as part of a study into the effect of weightlessness on their sex lives and development.
“We can say with confidence that they died at least a week before the landing because their bodies were partly mummified,” an official from Russia’s Institute of Medical and Biological Problems told Itar-Tass news agency.
The Russian space agency has not yet outlined the cause of death.
But Interfax news agency, quoting an expert working on the mission, says preliminary data shows the geckos may have died after a malfunction with the satellite’s heating system.
Drosophila fruit flies that were also travelling on the satellite, however, survived and had reproduced, Roscosmos said.
Mushrooms and plant seeds were also being monitored as part of the experiment, while a special vacuum furnace was used to examine the melting and solidification of metal alloys in low-gravity conditions.
The six-tonne satellite was launched on 19 July and was meant to carry out experiments over a two-month period. However, it returned after just 44 days in orbit.
Soon after its launch, Roscosmos briefly lost contact with the satellite when the Foton-M4’s engine stopped responding to ground control.