The animals, aged between three and eight weeks, were taken by gardai and officers from the Dublin Society for the Prevention of Cruelty to Animals.
It followed searches of two cars on October 9, on the Old Malahide Road in the Coolock area in north Dublin.
The puppies were in boxes in the back of both vehicles and included a number of Cocker and Springer spaniels, terrier, beagle, and Labrador breeds along with several Jack Russells.
Two men, Reuben Burton (32) and his brother Rico Lee Burton (21), both from Manchester, have been charged under the Protection of Animals Act.
It is alleged they ill-treated animals by keeping 50 pups in the back of cars "in cramped conditions with no food or water, no light or fresh air ... causing unnecessary suffering".
The brothers are due back before the court in January for DPP's directions on the charges.