Once she said was scared to death of Tongo the Apeman.

Any other times?

Mary Ann,Ginger and Mrs.Howell were affraid of the headhunters,
they said to Gilligan that don't want to be left alone in the ep:
Music Hatch charm.

Mary Ann was affraid in the ep:The Postman Cometh.When
she thought she was going to dye!

Mary Ann,Ginger and Mr.Howell were scared of the lion in
the ep:Feed the Kitty.

Mary Ann and Ginger were scared of the witch doctor in
the ep:Voodoo.

Mary Ann was scared when the gorilla grab her in the ep:
Diamonds are an Ape's Best Friend.

I seem to recall Maryann being frightened when Jonathan Kinkade pointed his gun at her. She said a real terrified "Me?".

Maryann being scared of the giant skipper (episode #66, V FOR VITAMINS, 4/14/1966, w:Barney Slater, d:Jack Arnold), of Johnahtna Kincaid (Rory Calhoun) that the previous poster noted (episode #86,THE HUNTER,1/16/1967,w:William Gershman and Ben Freedman,d:Leslie Goodwins), and she's frightneed of Gilligan's weird behavior when he;'s about to cut off the totem pole head (episode #91, HIGH MAN ON THE TOTEM POLE, 2/27/1967,w:Brad Radnitz,d:Herbert Coleman).

And she was worried about being made into "a pretzel"(episode #65, THE FRIENDLY PHYSICIAN guest-starring Vito Scotti & Mike Mazurki, 4/07/1966, w:Elroy Schwartz, d:Jack Arnold) and throughout her own episode about mushrooms and her "boyfriend",Horace Higgenbothem (episode #55, THE POSTMAN COMETH, 1/13?/1966, w:Alan Dinehart and Herbert Finn, d:Leslie Goodwins)."Young Dr.Young!!" And many other times May Ann became frightened.