If im in third trimester of pregnancy is it safe to take Flagyl for amobeas?

Amebas not friendly. The risk of getting sick with amebiasis is very high.
Yes if Benefit>Risk. As long as you past the first trimester, the time when the internal organs first form in the fetus, the dangers of taking Metronidazole (brand name: flagyl) is minimized. Metronidazole use in the second and third trimesters of pregnancy should be used when alternative, safer treatment is either unavailable or is inadequate. Your doctor will guide your decision on this important issue.