Jaboticaba (Myrciaria cauliflora) and false jaboticaba (Myrciaria vexator) fruits are two pleasant-tasting, dark-colored fruits, native to Brazil. They are rich sources of phenolic compounds, including anthocyanins, flavonoids, phenolic acids, and tannins, as well as less well known polyphenols such as depsides. These two fruits are very similar in morphology, but their taste profiles differ markedly. This study was focused on identifying the marker compounds between them using HPLC-PDA and LC-TOF-MS, combined with principal component analysis. As a result, cyanidin-3-O-glucoside was found as the major anthocyanin in Myrciaria fruits. Delphinidin-3-O-glucoside was found to be the marker compound for jaboticaba, while cyanidin-3-O-galactoside and cyanidin-3-O-arabinose were two marker compounds distinguishing false jaboticaba. In addition, two ellagitannins, iso-oenothein C and oenothein C, were isolated and identified from both of these fruits for the first time. Jaboticabin, a minor bioactive depside, occurred in both fruits and, because of its potential to treat chronic obstructive pulmonary disease, was successfully synthesized in the laboratory.