Hans Kubus, 58, was stopped at Christchurch Airport on Sunday after checking in, and was searched by customs staff.
A small package containing the reptiles was found in his underwear, prosecutor Mike Bodie told the Christchurch District Court on Monday.
"The package contained eight separate compartments separating various gecko and skink species," he said.
Kubus' luggage also contained a single gecko in a rolled up sock.
A total of 24 geckos were found from five different species, as well as 20 skinks from two species.
The German admitted trading geckos and taking geckos and skinks from the wild without a permit.
A black market trade in geckos exists in Europe and those taken by Kubus would have had a street value of around $35,850 US, Bodie said.
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The value of the skinks was unknown because trading in that species had not previously been identified.
Kubus was due to be sentenced on January 25.