To stop your male dog from marking his territory in the house, you first need to understand why he is doing it. A male dog will instinctively mark his territory to protect it from a perceived threat as well as to build his confidence. Particularly when there are new developments in the house such as visitors, a new baby or a new pet your male dog is more likely to mark his territory. While it is most certainly a frustrating behavior, remember that your male dog is marking his territory because he wants to protect his family.
Have your male dog neutered by a veterinarian. An intact male dog is much more likely to mark his territory inside the home than a neutered one.
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Supervise your male dog at all times in the house while you are training him not to mark. Confine him in a comfortable crate when you are unable to supervise and correct his marking behavior.
Use a belly band to catch urine and to discourage territorial marking. Kathy Diamond Davis, author of the book "Therapy Dogs: Training Your Dog to Reach Others" believes that belly bands may actually bring the dog's attention to an instinctive behavior thereby possibly reducing marking behavior.
Interrupt territorial marking and take your dog outside. Give your dog praise when he urinates appropriately. Never punish your male dog for territorial marking, it will only harm your relationship.
Clean soiled areas with pet enzyme products and if possible restrict your dog's access to these areas. If this is not possible, remove territorial triggers such as food and water, the toy basket or beds.
Establish yourself as the leader in your relationship with your male dog. According to the "Nothing in Life Is Free Training Method" of the Sacramento SPCA, establishing yourself as the leader with your dog will help stabilize the relational hierarchy and reduce your male dog's drive to mark his territory.
Consult your veterinarian for advice and direction. Your veterinarian can refer you to a dog behaviorist or trainer for help.