Estimation of arrival angles and incoming signals is a challenging problem for HF channels where the signals are correlated and the separation between the signals can be as low as a couple of degrees. In this paper, a new algorithm, Multipath Separation-Direction of Arrival (MS-DOA), is developed to estimate both the arrival angles in elevation and azimuth and the incoming signals at the output of the reference antenna with very high accuracy. The MS-DOA algorithm provides reliable angle and signal estimates even with small separation of arrival angles and for low SNRs. The minimum number of antennas that are required by the algorithm is only one more than the number of incoming signals. In a narrowed down region of interest and for a few incoming signals, the computational search time for MS-DOA is only a couple of minutes in a standard PC.