I used to worry mainly around dusk and dawn, where I'd always wear long pants and shirtsleeve to make attack by marauding mosquitoes somewhat more difficult. Unfortunately the vector for Chikungunya (Aedes aegypti) is also a day feeder, so that preventative measure doesn't work all that well.
While using DEET or other sprays/salves is an alternative for short stays, I'm there 6 months of the year so prefer not to; and fortunately most of the time the winds in the anchorages do a great job at ensuring mosquito-free zones aboard.