What is the best time of the day to take doxyxycline 100mg? i am taking it indefinitely for treatment of my chronic dry eye.

Doesn't matter: That's a high dose for chronic maintenance of dry eye. A dose of 25 or 50 mg is more common. The time of day is not important with this medication but you should avoid dairy products or any calcium containing supplements for an hour or two before and after taking this medication.

Doxycycline: Low does Doxycycline 20mg/d helps chronic dry eye (an inflammatory disease often) by inhibiting inflammatory factors (ie mmps) with a mechanism which is independent from their antibiotic effect. You can take it any time during day. It absorbs well with food though recommend avoid taking with calcium rich foods.

Does not matter: However, have you considered other options rather than taking doxy indefinitely, such as pulsing with Azasite drops, using warm compresses and lid massages, or even taking omega-3's orally? Also, Restasis and punctal plugs could give you more tears as well. Lastly, you should not be taking doxy if you are pregnant.