Addiction management is complex, and it requires a bio-psycho-social perspective, that ought to consider the multiple etiological and developmental factors. Because of this, a large amount of resources has been allocated to assess the vulnerability to dependence, i.e., to identify the processes underlying the transition from substance use to dependence, as well as its course, in order to determine the key points in its prevention, treatment, and recovery. Consequently, knowledge \from neuroscience must be taken into account, which is why different initiatives have emerged with this objective, such as the "Research Domain Criteria" (RDoC), and the "Addiction Neuroclinical Assessment" (ANA). Particularly, neuropsychophysiological measures could be used as markers of cognitive and behavioral attributes or traits in alcohol dependence, and even trace clinical change. In this way, the aim of this narrative review is to provide an overview following ANA clinical framework, to the most robust findings in neuropsychophysiological changes in alcohol dependence, that underlie the main cognitive domains implicated in addiction: incentive salience, negative emotionality, and executive functioning. The most consistent results have been found in event-related potential (ERP) analysis, especially in the P3 component, that could show a wide clinical utility, mainly for the executive functions. The review also shows the usefulness of other components, implicated in affective and substance-related processing (P1, N1, or the late positive potential LPP), as well as event-related oscillations, such as theta power, with a possible use as vulnerability or clinical marker in alcohol dependence. Finally, new tools emerging from psychophysiology research, based on functional connectivity or brain graph analysis could help toward a better understanding of altered circuits in alcohol dependence, as well as communication efficiency and effort during mental operations. This review concludes with an examination of these tools as possible markers in the clinical field and discusses methodological differences, the need for more replicability studies and incipient lines of work. It also uses consistent findings in psychophysiology to draw possible treatment targets and cognitive profiles in alcohol dependence.