Combine the vinegar and sugar in a saucepan and stir over medium heat until the sugar dissolves. Mix in the carrot and red pepper. Bring to a boil and boil for 5 minutes. Add the Habanero and boil for an additional 5 minutes.
Remove from the heat, add the pectin, return to a boil for 1 minute, stirring constantly. Skim off any foam and bottle in sterilized 4 ounce jelly jars.
