The box included bags of snakes, spiders, frogs and lizards
The Kenya Wildlife Service says it has intercepted an illegal shipment of live snakes before it was loaded on to a plane in Mombasa bound for Japan.
The box had 113 animals altogether, including reptiles, frogs and spiders.
Interpol officials in Germany later intercepted another consignment containing 338 live reptiles that had already left Mombasa.
The BBC's Odhiambo Joseph in Mombasa says two men have been arrested and the shipment impounded at the airport.
One of the men, the director of a reptile farm located south of Mombasa, is said to be a German national.
The KWS says that according to its records, the farm has a temporary licence but has no permit to export the animals as required by the law.
KWS official Philip Mwakio told the BBC that they had received a tip-off about the planned shipment early on Thursday.
The box has been impounded at Moi International Airport in Mombasa
"We laid our trap and we had our officers there at the airport and when this box came," Mr Mwakio said.
"When we inspected, we had two spiders, we had one terrapin, we had one tree frog, we had two geckos and the remaining were an assortment of species of snakes."
He said the illicit trade in live animals was a big problem in Kenya.
"There is an underground business which is being done with this type of species of animals," Mr Mwakio said.
"It is something which we have been following for quite some time now."
Kenya is now seeking the assistance of Interpol to help curb the export of snakes, frogs, spiders and geckos, our reporter says.