In the late twentieth century, the term “System of Systems” (SoS) became popular to describe a complex system made up of a combination of independent constituent systems. Since then, several studies have been conducted to support and assess SoS management, functionality, and performance. Due to the evolutionary nature of SoS and the non-composability of the security properties of its constituent systems, it is difficult to assess or evaluate SoS security. This paper provides an up-to-date survey on SoS security, aimed at stimulating and guiding further research efforts. This systematic mapping study (SMS) focuses on SoS security, privacy, and trust. Our SMS identified 1828 studies from 6 digital libraries, 87 of which were selected that presented approaches analyzing, evaluating, or improving security. We classified these studies using nine research questions that focused on the nature of the studies, the studied SoS, or the study validation. After examining the selected studies, we identified six gaps and as many future work directions. More precisely, we observed that few studies examine SoS problems and instead propose specific solutions, making it challenging to develop generalizable approaches. Furthermore, the lack of standardization has hindered the reuse of existing approaches, making it difficult for solutions to be generalized to other SoS. In addition, the lack of descriptions of industrial environments in the literature makes it difficult to design realistic validation environments. As a result, the validation of new SoS research remains a challenge in the field.