Establishing quantifiable biological markers associated with anxiety will increase the objectivity of phenotyping and enhance genetic research of anxiety disorders. Heart rate variability (HRV) is a physiological measure reflecting the dynamic relationship between the sympathetic and parasympathetic nervous systems, and is a promising target for further investigation. This review summarizes evidence evaluating HRV as a potential physiological biomarker of anxiety disorders by highlighting literature related to anxiety and HRV combined with investigations of endophenotypes, neuroimaging, treatment response, and genetics. Deficient HRV shows promise as an endophenotype of pathological anxiety and may serve as a noninvasive index of prefrontal cortical control over the amygdala, and potentially aid with treatment outcome prediction. We propose that the genetics of HRV can be used to enhance the understanding of the genetics of pathological anxiety for etiological investigations and treatment prediction. Given the anxiety–HRV link, strategies are offered to advance genetic analytical approaches, including the use of polygenic methods, wearable devices, and pharmacogenetic study designs. Overall, HRV shows promising support as a physiological biomarker of pathological anxiety, potentially in a transdiagnostic manner, with the heart–brain entwinement providing a novel approach to advance anxiety treatment development. This review proposes that the genetics of heart rate variability (HRV) can be used to identify novel treatment targets for anxiety disorders given that impaired HRV has support as an anxiety endophenotype, reflects anxiety‐related brain activation patterns, and may predict treatment response. Advanced approaches such as use of wearables to collect large samples, polygenic risk score methods, and pharmacogenetics are suggested to develop HRV genetic research. [ABSTRACT FROM AUTHOR]