It is safe to use melatonin only at night for thunderstorm phobia. Don't use melatonin during the day since it can throw off the natural biorhythm and do more harm than good.
During the day you can use Bach's Rescue Remedy, or a herbal anti-anxiety formula that contains: hops, passionflower, valerian, and poppy. If the herbal's are ineffective, than it would be best to get a prescription medication from your dog's vet.
thank you so much! at night is when i need it during the day i can handle her! i just play with her and distract her from the storm then. but night time intensifies her fear and she is just inconsolable.