The pup's owner, Anthony and Andrea Baerga, say they came back to the store around 5 p.m. Thursday to pick up the dogs. The shop had closed, but there was a sign on the front door instructing them to go around back.
An employee was there to return one of his dogs, but the other, a black poodle named Bodie, was nowhere to be found.
"We just want our dog back, that's all we want," said Andrea Baerga.
The owners say Bodie may be partially shaved.
The owner of the pet shop, Guy Guillen, apologized in a statement on his Facebook page.
"The dog had been ... put back in (a) cage, not sure what happened, if gate was not latched correctly or not, but dog would have had to get out of two doors," Guillen said. "It's the most horrific thing I have ever dealt with ... To the family, my sincere apologies. I pray Bodie is found."