This research aimed to study and compare prevalence of work-related musculoskeletal (MSK) problem and perceived discomfort among port crane operators consisting of quay and rubber tyred gantry (RTG) cranes working in the Laem Chabang Deep-sea Port, Thailand. Direct interviews for a cross-sectional analysis was selected for this unique job with a small amount of sample size. A standardized modified version of the Nordic Musculoskeletal Questionnaire (NMQ) was lunched for 26 male participants, consisting of 11 quay and 15 RTG, where a priori power analysis using G*Power suggested the minimum as 24 for the hypothesis test. Socio-demographic characteristics showed no significant difference among them. The NMQ revealed lower back as the highest prevalent body part (76.9%) followed by neck, shoulders and upper back at the same percentage (23.1%) for all port crane group, with up to 96.2% reporting MSK problem over the past 12 months. And Borg scale rating, assessing the perceived discomfort, revealed lower back with the highest score (2.38) followed by upper back (0.65), shoulders (0.54) and neck (0.5). Remarkably, the comparation between the quey and RTG crane operators on the MSK prevalence (χ2 test) and perceived discomfort levels (Kruskal-Wallis test), regarding different 9 body parts, revealed a significant difference between the two on upper back with quay crane having more problem than the RTG at p < 0.05. while the rest of them were mainly in the same direction. MSK contributors such as: working awkward posture, mental stress, height, trolley distance and vibration are considerably the main causes of this. However, the larger in scale of exposure to those for the quey crane compared to the RTG might have led to the distinguishing MSK problem found in this study which require thoroughly deliberation for the particular solutions.