The Customs and Border Protection Service said the men, aged 38 and 33, were selected for a baggage examination when they recently checked in at Perth International Airport.
During an x-ray search, officials found 28 shingleback lizards, another unspecified skink and one bearded dragon.
Western Australia Department of Parks and Wildlife senior wildlife investigator Rick Dawson said the haul was worth more than Aus$130,000 (US$122,000)
“These lizards are highly sought-after in Asia because they are easy to care for, attractive, and exotic,” he said.
The protected Rottnest Island shingleback lizards are worth up to Aus$8,000 each on the Asian black market, while mainland shinglebacks fetch Aus$4,000 or more, depending on their colour forms.
Dragons and other skinks go for around Aus$1,000.
The men face a range of charges including unlawfully taking protected fauna and subjecting a protected species to cruel treatment.
They could face up to 10 years in jail and fines of up to Aus$170,000.