The aim was to investigate mortality among Swedish seafarers compared to the general population, and differences in mortality between occupational categories and differences over time. Longitudinal register-based cohort study of 85,169 Swedish seafarers registered in the Swedish Transport Agency's Seafarers' Registry (SR) 1985-2013. The cohort was matched with the Swedish Cause of Death Register. Standardized mortality ratios (SMRs) and 95% confidence intervals (CIs) were calculated stratified by gender, job category, start of sea service, and time registered in the SR. Seafarers were followed until 66 years of age. Mortality by diseases was analyzed for seafarers with at least 5 years of sea service and mortality due to external causes was analyzed for all seafarers. Total mortality was increased among men who started to work before 1985 (SMR: 1.27, 95% CI: 1.21-1.32) and borderline significantly increased among women (SMR: 1.14, 95% CI: 0.99-1.32). Mortality ratios due to lung cancer, accidents, suicides, and mental disorders including substance abuse, were increased among seafarers who started to work before 1985. Mortality risks were particularly increased among the crew. SMRs tended to decrease over time, but mortality due to accidents was still increased among the crew who started to work 1985 or later (SMR: 1.64, 95% CI: 1.02-2.63). Swedish seafarers had an increased mortality compared to the general population in 1985-2013, particularly the crew. There is still an increased mortality in accidents among crew who started to work 1985 or later.