Noise and decoherence are major obstacles to the implementation of Josephson junction qubits in quantum computing. Recent experiments suggest that two level systems (TLS) in the oxide tunnel barrier are a source of decoherence. We explore two decoherence mechanisms in which these two level systems lead to the decay of Rabi oscillations that result when Josephson junction qubits are subjected to strong microwave driving. (A) We consider a Josephson qubit coupled resonantly to a two level system, i.e., the qubit and TLS have equal energy splittings. As a result of this resonant interaction, the occupation probability of the excited state of the qubit exhibits beating.