Swallowing is a complex sequence of highly regulated and coordinated skeletal and smooth muscle activity. Previous studies have attempted to determine the temporal relationship between the muscles to establish the activation sequence pattern, assessing functional muscle coordination with cross-correlation or coherence, which is seriously impaired by volume conduction. In the present work, we used conditional Granger causality from surface electromyography signals to analyse the directed functional coordination between different swallowing muscles in both healthy and dysphagic subjects ingesting saliva, water, and yoghurt boluses. In healthy individuals, both bilateral and ipsilateral muscles showed higher coupling strength than contralateral muscles. We also found a dominant downward direction in ipsilateral supra and infrahyoid muscles. In dysphagic subjects, we found a significantly higher right-to-left infrahyoid, right ipsilateral infra-to-suprahyoid, and left ipsilateral supra-to-infrahyoid interactions, in addition to significant differences in the left ipsilateral muscles between bolus types. Our results suggest that the functional coordination analysis of swallowing muscles contains relevant information on the swallowing process and possible dysfunctions associated with dysphagia, indicating that it could potentially be used to assess the progress of the disease or the effectiveness of rehabilitation therapies.