In general, the performance of a direction of arrival (DOA) estimator may decay under a non-uniform noise and low signal-to-noise ratio (SNR) environment. In this paper, a memetic particle swarm optimization (MPSO) algorithm combined with a noise variance estimator is proposed, in order to address this issue. The MPSO incorporates re-estimation of the noise variance and iterated local search algorithms into the particle swarm optimization (PSO) algorithm, resulting in higher efficiency and a reduction in non-uniform noise effects under a low SNR. The MPSO procedure is as follows: PSO is initially utilized to evaluate the signal DOA using a subspace maximum-likelihood (SML) method. Next, the best position of the swarm to estimate the noise variance is determined and the iterated local search algorithm to reduce the non-uniform noise effect is built. The proposed method uses the SML criterion to rebuild the noise variance for the iterated local search algorithm, in order to reduce non-uniform noise effects. Simulation experiments confirm that the DOA estimation methods are valid in a high SNR environment, but in a low SNR and non-uniform noise environment, the performance becomes poor because of the confusion between noise and signal sources. The proposed method incorporates the re-estimation of noise variance and an iterated local search algorithm in the PSO. This method is effectively improved by the ability to reduce estimation deviation in low SNR and non-uniform environments.