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The high frequency (HF) band lies within 2-30 MHz of the electromagnetic spectrum. For decades, the HF band has been recognized as the primary means of long-range wireless communications. When satellite communication first emerged in 1960s, HF technology was considered to be obsolete. However, with its enduring qualities, HF communication survived through this competition and positioned itself as a powerful complementary and/or alternative technology to satellite communications. HF systems have been traditionally associated with low-rate data transmission. With the shift from analog to digital in voice communication, and increasing demands for high-rate data transmission (e.g., e-mail, Internet, FTP), HF communication has been going through a renaissance. Innovative techniques are required to push the capacity limits of the HF band. In this dissertation, we consider cooperative communication as an enabling technology to meet the challenging expectations of future generation HF communication systems. Cooperative communication exploits the broadcast nature of wireless transmission and relies on the cooperation of users relaying the information to one another. We address the design, analysis, and optimization of cooperative HF communication systems considering both multi-carrier and single-carrier architectures. As the multi-carrier HF system, we consider the combination of the orthogonal frequency division multiplexing (OFDM) with the bit interleaved coded modulation (BICM) as the underlying physical layer platform. It is assumed that cooperating nodes may use different HF propagation mechanisms, such as near-vertical-incidence sky wave (NVIS) and surface wave, to relay their received signals to the destination in different environmental scenarios. Diversity gain analysis, optimum relay selection strategy and power allocation between the source and relays are investigated for the proposed cooperative HF system. For single-carrier HF systems, we first derive a matched-filer-bound (MFB) on the error rate performance of the non-regenerative cooperative systems. The results from the MFB analysis are also used for relay selection and power allocation in the multi-relay cooperative systems. To overcome the intersymbol interference impairment induced by frequency-selectivity of the HF channel, equalization is inevitable at the destination in a single-carrier system. In this work, we investigate the minimum-mean-square-error (MMSE) based linear/decision-feedback frequency domain equalizers (FDEs). Both symbol-spaced and fractionally-spaced implementations of the proposed FDEs are considered and their performance is compared under different channel conditions and sampling phase errors at the relay and destination nodes.