This paper examines hybrid threats to maritime transportation systems and their governance responses; focusing on the congested Straits of Malacca and Singapore (SOMS) as an illustrative case study. The methodology combines secondary sources with primary data from 42 expert interviews, a 28 respondent survey, and two maritime security roundtables. Key findings were that ships’ critical systems are increasingly interconnected, yet aging IT infrastructure and minimal cybersecurity awareness among crews heighten risks. Meanwhile, regional terrorist groups have previously targeted shipping and shown considerable skill in exploiting online tools, aligning with broader calls for jihadist violence. Furthermore, opportunistic piracy persists in the SOMS with the potential to disrupt shipping. Experts confirmed that maritime cybersecurity lags behind other critical infrastructure sectors and needs updated governance. Initial International Maritime Organization (IMO) guidelines lack specificity but revisions and updated IMO guidance are in process, while Port state implementation of maritime cybersecurity standards varies. Crucially, information sharing remains inadequate, even as recorded attacks increase. Findings underscore that although major hybrid incidents have not occurred, simulations and threat actors’ capabilities demonstrate potential for catastrophic collisions or cascading disruption in congested waterways. Mitigating factors like redundancy and crew training are deficient currently. Some alignment between SOMS states on maritime security cooperation exists, but not on cyber threats specifically. Key recommendations include an anonymous cyber attack reporting system, reinforced training and shipboard systems, and consolidated regional frameworks. Until these priorities are addressed, the analysis concludes that hybrid vulnerabilities in this vital global chokepoint remain a serious concern.