"It has outlived another gecko which used to share its terrarium.
"The police have been notified, and we are asking everyone to keep their eyes open."
The terrarium is near the entrance to the visitor centre in Southland and was refreshed with food and leaves mid-afternoon on 16 July.
When the ranger returned three days later, the padlock had been removed and the gecko was missing, Mr Lind said.
Senior ranger Kate Hebblethwaite said staff were "just devastated" by the apparent theft.
"I am not sure what would possess someone to do something like this."
The Marlborough green gecko, also known as the manuka gecko, is endemic to New Zealand. It can grow up to 70mm long and is classified as an At Risk species.
• Anyone with information about the missing gecko should contact Te Anau police or the Te Anau Doc office (03) 249-0200.