Dogen's poison was a small viridian-colored capsule that Dogen himself prepared using various unknown ingredients and a pestle and mortar. ("What Kate Does")
Dogen's intention was to get Jack to give the capsule to Sayid in an attempt to eliminate the yet unknown infection that the TempleOthers believed Sayid had contracted.
Jack refused to give Sayid the capsule and swallowed it himself in an extreme attempt to get Dogen to tell him the truth about the capsule. Dogen physically attacked Jack and performed the Heimlich maneuver before Jack could swallow the capsule. Dogen then reluctantly told Jack that the capsule was poison.