Investigators believe the men were stealing gift cards, peeling back the scratch protectors and copying down activation codes and serial numbers before returning the cards to store shelves.
They were then able to make online purchases using the codes after customers bought the cards and loaded them with money.
The Texas Financial Crimes Intelligence Center began investigating March 17 after employees at the Walgreens on Kuykendahl and FM 2920 in Spring saw a man hanging around the gift card display and then found 15 altered gift cards.
Investigators say the same man was seen at other Walgreens, CVS and Dollar Tree stores with accomplices.
On March 20, they say he visited 22 Houston area stores in a rented car and stole more than 1,000 gift cards.
According to a search warrant, the thefts continued March 30 at 31 Austin area stores.
The next day, investigators arrested Houjie Lin and Yi-Hsun Wu at a Walgreens in Buda, Texas.
They say they found 80 gift cards in the suspects' car as well as two Taiwanese passports.
When they searched the suspects' Austin hotel room on April 1, they say they found more than 3,000 gift cards.
Investigators believe the theft ring was operating out of a home in Sharpstown. During an April 10 search, they said they found 277 bundles of gift cards.
No one answered when Eyewitness News knocked Saturday.
Records show Lin has since bonded out of the Hays County Jail while Wu is being held by ICE.