As a preliminary study, we have found that honey from manuka (Leptospermum scoparium) in New Zealand inhibits myeloperoxidase (MPO) activity. In this study, using a chromatographic technique, we isolated two active compounds for MPO-inhibition from manuka honey. One is methyl syringate (MSYR), and the other was identified as a novel glycoside of MSYR, methyl syringate 4-O-β-d-gentiobiose, which has been named “leptosin” after the genus Leptospermum. The amount of the glycoside ranged from 0.2 to 1.2 μmol/g honey. Leptosin was only found in honeys from the Oceania region, and abundantly in manuka honey including jelly bush honey from Leptospermum polygalifolium in Australia. Therefore, leptosin may be a good chemical marker for manuka honey. Interestingly, the concentration of leptosin in manuka honey was positively correlated with the unique manuka factor (UMF) value, which is expressed as phenol equivalents of its bactericidal activity.