Communication with remote places is a challenge often solved using satellites. However, when trying to reach Antarctic stations, this solution suffers from poor visibility range and high operational costs. In such scenarios, skywave ionospheric communication systems represent a good alternative to satellite communications. The Research Group in Electromagnetism and Communications (GRECO) is designing an HF system for long haul digital communication between the Antarctic Spanish Base in Livingston Island (62.6S, 60.4W) and Observatori de l’Ebre in Spain (40.8N,0.5E) (Vilella et al., 2008). The main interest of Observatori de l’Ebre is the transmission of the data collected from the sensors located at the base, including a geomagnetic sensor, a vertical incidence ionosonde, an oblique incidence ionosonde and a GNSS receiver. The geomagnetic sensor, the vertical incidence ionosonde and the GNSS receiver are commercial solutions from third parties. The oblique incidence ionosonde, used to sound the ionospheric channel between Antarctica and Spain, was developed by the GRECO in the framework of this project. During the last Antarctic campaign, exhaustive measurements of the HF channel characteristics were performed, which allowed us to determine parameters such as availability, SNR, delay and Doppler spread, etc. In addition to the scientific interest of this sounding, a further objective of the project is the establishment of a backup link for data transmission from the remote sensors in the Antarctica. In this scenario, ionospheric communications appear to be an interesting complementary alternative to geostationary satellite communications since the latter are expensive and not always available from high-latitudes. Research work in the field of fuzzy logics applied to the estimation of the above mentioned channel was first applied in (Alsina et al., 2005a) for serial search acquisition systems in AWGN channels, afterwards applied to the same channel but in the multiresolutive structure (Alsina et al., 2009a; Morán et al., 2001) in papers (Alsina et al., 2007b; 2009b) achieving good results. In this chapter the application of fuzzy logic control trained for Rayleigh fading channels (Proakis, 1995) with Direct-Sequence Spread-Spectrum (DS-SS) is presented, specifically suited for the ionospheric channel Antarctica-Spain. Stability and reliability of the reception, which are currently being designed, are key factors for the reception. It is important to note that the fuzzy control design presented in this chapter not only resolves the issue of improving the multiresolutive structure performance presented by (Morán et al., 2001), but also introduces a new option for the control design of many LMS adaptive structures used for PN code acquisition found in the literature. (El-Tarhuni & Sheikh, 1996) presented an LMS-based system to acquire a DS-SS system in Rayleigh channels; years after, (Han et al., 2006) improved the performance of the acquisition system designed by (El-Tarhuni & Sheikh, 1996). And also in other type of channels, LMS filters are used as an acquisition system, even in oceanic transmissions (Stojanovic & Freitag, 2003). Although the fuzzy control system presented in this chapter is compared to the stability control used in (Morán et al., 2001) it also can be used to improve all previous designs performance in terms of stability and robustness. Despite this generalization, the design of every control system should be done according to the requirements of the acquisition system and the specific channel characteristics.