I know of one ingredient called Silphium that is currently lost to the world and was used during the time of the Roman Empire excessively as a contraceptive, medicinal aid and sometimes as an ingredient in cooking. It was grown in coastal areas of Cyrene (modern day Libya) and was a staple of their economy before its extinction and was traded north to Romans under heavy demand.

It is talked about in the Apicus, a collection of Greco-Roman recipes, and even after it's extinction it was still noted in many collections and lists of various aromatics. The identity and plant itself is lost to history, but it made quite the mark on the world: with Cyrene coinage depicting the plant and some believing the heart symbol is based off of the seedpods of the plant.

The Roman 'recipe' is incredibly strange, much briefer than its modern counterpart. Recipes don't give quantities or timings and very few have serving suggestions. If anything, these recipes are a reminder for the trained cook preparing them. As such, you could argue that even those dishes which we do have recipes for are still unknown entities.

You can see a selection of Roman recipes (and modern recreations) on Pass the Garum. /u/A_Wooper is right to mention Silphium, an ingredient farmed to extinction if the stories are to be believed - all we have now is a distant cousin and therefore an approximation of the taste of the original.

One of the recipes which I've had to 'guess' is Posca, a vinegar-based drink.