Recently, markerless tracking systems, such as RGB-Depth cameras, have spread to overcome some of the limitations of the gold standard marker-based tracking systems. Although these systems are valuable substitutes for human motion analysis, as they guarantee higher flexibility, faster setup time and lower costs, their tracking accuracy is lower with respect to marker-based systems. Many studies quantified the error made by markerless systems in terms of body segment length estimation, articular angles, and biomechanics, concluding that they are appropriate for many clinical applications related to motion analysis. We propose an innovative approach to compare a markerless tracking system (Kinect V2) with a gold standard marker-based system (Vicon), based on motor control assessment. We quantified kinematic synergies from the tracking data of fifteen participants performing multi-directional upper limb movements. Kinematic synergy analysis decomposes the kinematic data into a reduced set of motor primitives that describe how the central nervous system coordinates motion at spatial and temporal level. Synergies were extracted with the recently released mixed-matrix factorization algorithm. Four synergies were extracted from both marker-based and markerless datasets and synergies were grouped in 6 clusters for each dataset. Cosine similarity in each cluster was ⩾0.60 in both systems, showing good consistency of synergies. Good matching was found between synergies extracted from markerless and from marker-based data, with a cosine similarity between matched synergies ⩾0.60 in 5 out 6 synergies. These results showed that the markerless sensor can be feasible for kinematic synergy analysis for gross movements, as it correctly estimates the number of synergies and in most cases also their spatial and temporal organization.