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We explore complex dynamic patterns of autonomic physiological linkage (i.e., statistical interdependence of partner’s physiology; PL), within the sympathetic and parasympathetic nervous systems (SNS and PNS), as potential correlates of emotional and regulatory dynamics in close relationships. We include electrodermal activity (EDA) as an indicator of SNS activation and respiratory sinus arrhythmia (RSA) as an indicator of regulatory and/or homeostatic processes within the PNS. Measures of EDA and RSA were collected in 10-second increments from 53 heterosexual couples during a mixed-emotion conversation in the laboratory. We used the R statistical package, rties (Butler & Barnard, 2019), to model the dynamics of EDA and RSA with a coupled oscillator model and then categorized couples into qualitatively distinct profiles based on the set of parameters that emerged. We identified two patterns for EDA and three patterns for RSA. We then investigated associations between the PL patterns and self-report measures of relationship and conversation quality and emotional valence using Bayesian multilevel and logistic regression models. Overall, we found robust results indicating that PL profiles were credibly predicted by valence and relationship quality reported prior to the conversations. In contrast, we found very little evidence suggesting that PL patterns predict self-reported conversation quality or valence following the conversation. Together, these results suggest that PL across autonomic subsystems may reflect different processes and therefore have different implications when considering interpersonal dynamics.