Martin, speaking from a wheelchair, apologized for his actions, saying he had "made mistakes" but that admission did not satisfy Jones.
"I think you are sorry you got caught," said Jones, adding he would have given him the maximum 14-month sentence, but took into account that Martin suffers from multiple sclerosis.
Susan Martin was sentenced to three years' probation.
The two were ordered to pay $300,000 in restitution to the U.S. Department of Agriculture to be used for animal-welfare work.
Under a deal with prosecutors, Floyd Martin pleaded guilty to one count of mail fraud, while Susan Martin pleaded guilty to a count of conspiracy,
The Martins, who are Mennonite, operated Chestnut Grove Kennel in Shippensburg and were licensed by the federal government as Class B or "random source" animal dealers.
Class B dealers may purchase dogs from unlicensed individuals who collect dogs - "bunchers" - but those individuals may sell the dealers no more than 24 dogs a year.
According to the indictment, the Martins purchased hundreds of dogs from just two individuals while falsely certifying to the U.S. Department of Agriculture that they had purchased fewer than 25 dogs from multiple family members and friends - including one person who was deceased by the time of the alleged sale.
The Martins then sold the dogs to hospitals, among them Johns Hopkins, and other research facilities for hundreds of dollars in profit per dog, the indictment said.
About 3,100 dogs, or 3 percent of those used in biomedical research in the United States, come from random-source dealers, federal data show, down from tens of thousands 15 years ago.
Many research facilities, most notably the National Institutes of Health have moved away from use of random-source dogs, as attitudes on use of animals in testing has shifted and pressure has mounted against experimenting on animals that may have once been pets.
"The industry is dying on the vine," said Nancy Blaney, senior policy adviser for the Animal Welfare Institute, the Washington group that has focused on exposing the underworld of animal dealing.
She said only about six Class B dealers remain nationwide and several of those are under federal investigation.
"Dealers like the Martins and others thumbed their nose at the law for so long," she said. "The sentence is a good signal to those who remain that the government takes this fraud seriously and as a result takes animal cruelty seriously as well."
Rep. Michael Doyle (D., Pa.) has introduced a bill in Congress that would ban random-source dealers.
Contact Amy Worden at 717-783-2584 or firstname.lastname@example.org or follow #@inkyamy on Twitter.