Infant-mother behavioral synchrony is thought to scaffold the development of self-regulation in the first years of life. During this time, infants' and mothers' physiological regulation may contribute to dyadic synchrony and, in infants, dyadic synchrony may support infants' physiological regulation. Because the sympathetic nervous system (SNS) and parasympathetic nervous system (PNS) serve different regulatory functions, the current study aimed to elucidate relations between infants' and mothers' SNS and PNS functioning and dyadic behavioral synchrony. Skin conductance (SC; SNS index), respiratory sinus arrhythmia (RSA; PNS index), heart period (HP; index of joint SNS and PNS arousal), and behavioral synchrony were assessed in 6-month-old infants (N = 140) and their mothers during a mild social stressor, the Face-to-Face Still-Face paradigm (Tronick, Als, Adamson, Wise, & Brazelton, 1978). Synchrony was related to infants' and mothers' PNS and to mothers' broad autonomic arousal but not to SNS-specific arousal. Higher levels of behavioral synchrony were associated with lower infant RSA but with higher mother HP and RSA at baseline and in each Face-to-Face Still-Face paradigm episode. Therefore, lower RSA infants may have required more synchronous engagement with mothers to support regulation, while higher RSA, less aroused mothers may have been particularly well-attuned to infants' emotions. Findings suggest that each individual's physiological state may contribute to the behavioral functioning of the dyad.