Did you have a written agreement that he pay rent? If so, and he obtained the benefit of the rental agreement, I would expect that you would have the right to collect the unpaid rent, even though you may have been in breach of your agreement with your landlord. That said, small claims court can be a bit chaotic and judges can be more arbitrary than usual. Their decision is final, so there's always some risk that the judge doesn't see things your way.
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A subtenant in this position would not be making a very strong argument. Even if the agreement was in violation of the terms of the primary rental agreement, the subtenant still got the benefit of living in the home, and most judges will agree that the subtenant should not have been able to live there for free.
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