The purpose of this study was to compare baseball pitching kinematics measured with marker-less and marker-based motion capture. Two hundred and seventy-five fastball pitches were captured at 240 Hz simultaneously with a 9-camera marker-less system and a 12-camera marker system. The pitches were thrown by 30 baseball pitchers (age 17.1 ± 3.1 years). Data for each trial were time-synchronised between the two systems using the instant of ball release. Coefficients of Multiple Correlations (CMC) were computed to assess the similarity of waveforms between the two systems. Discrete measurements at foot contact, during arm cocking, and at ball release were compared between the systems using Bland-Altman plots and descriptive statistics. CMC values for the five time series analysed ranged from 0.88 to 0.97, indicating consistency in movement patterns between systems. Biases for discrete measurements ranged in magnitude from 0 to 16 degrees. Standard deviations of the differences between systems ranged from 0 to 14 degrees, while intraclass correlations ranged from 0.64 to 0.92. Thus, the marker-based and marker-less motion capture systems produced similar patterns for baseball pitching kinematics. However, based on the variations between the systems, it is recommended that a database of normative ranges be established for each system.