Vertebral column deviations, namely scoliosis, kyphosis, lordosis and combinations thereof, are poorly characterized in marine mammals. Here we present the clinical history and the post-mortem pathological and computed tomography (CT) scan analysis results on a 52-year-old captive female Antillean manatee (Trichechus manatus manatus) from Brazil. This animal had been kept at multiple small enclosures for most of its life. The main gross pathological and CT scan findings were severe thoracolumbar kyphoscoliosis that resulted in spinal canal stenosis and spinal cord compression. The adjacent thoracolumbar epaxial and hypaxial muscles were pale and atrophic. Acute and chronic myopathic changes, atrophy, as well as lipomatosis were confirmed microscopically. In this manatee, severe thoracolumbar kyphoscoliosis was probably triggered by captivity-related restricted mobility and postural and swimming alterations, including intermittent circling over decades. We surmise that postural, degenerative, spinal muscular/neuromuscular and muscle disuse atrophy occurred concurrently over time. These lesions probably resulted in sustained pain and could explain the behavioural alterations reported. This case sheds light on captivity-related vertebral column disease in sirenians and provides scientific evidence to inform housing recommendations for this taxon.