It is often said that, while Growlithe are the pets of Arceus, Houndour are the pets of Darkrai or Giratina – an explanation which was once taken literally. Others had theorized that the differences between Houndour and Growlithe come from them being different species before domestication, albeit related ones. Recent DNA sequencing, however, has demonstrated conclusively that Houndour were the result of crossbreeding between female Growlithe and a variety of dark-type pokemon over a period of many generations – and moreover, their molecular clocks demonstrated that this crossbreeding took place after domestication.
In other words, Houndour are as man-made as the pokeball, and their vicious treatment of strangers is nothing more than a manifestation of man's inhumanity towards their fellow man. This too has led to a variety of theories; some have thought them attack dogs, bred for war, their viciousness a means of making them better fighters. Others have thought them guards bred to protect their trainers from the ravages of psychics and the dead, their cruelty an unfortunate side effect. Perhaps they protected aristocratic estates in ancient times, or perhaps they worked with police or patrolled the borders of particularly isolationist villages.
When Houndour enter the historical record, they are found doing all these things, as well as acting as pets for those few who could tame and handle them – along with a sad number of those who couldn't. Which if any of these is their original purpose has been lost to history.