The objective of this study was to determine and compare the total phenolic content and antioxidant capacity in the seeds, skin, and pulp of eight cultivars of Florida-grown muscadine grapes and to identify the phenolic compounds in these respective portions. Total phenolic contents were determined colorimetrically using Folin-Ciocalteu reagent, and antioxidant capacity was determined by oxygen radical absorbance capacity (ORAC). High-performance liquid chromatography equipped with diode array (HPLC-DAD) and electrospray ionization mass spectrometric detection (ESI-MS(n)) was used to identify the phenolic compounds in the seeds, skin, and pulp of muscadine grapes. The total phenolic content and antioxidant capacity, based on fresh weight, were highest in seeds followed by skin and pulp. On average, 87.1, 11.3, and 1.6% of phenolic compounds were present in seeds, skin, and pulp, respectively. A total of 88 phenolic compounds of diverse structures were tentatively identified in muscadines, which included 17 in the pulp, 28 in the skin, and 43 in the seeds. Seventeen compounds were identified for the first time in muscadine grapes. The compounds identified in seeds included hydrolyzable tannins, flavan-3-ols and condensed tannins, ellagic acid derivatives, and quercetin rhamnoside. The skin contained hydrolyzable tannins, flavonoids, including anthocyanin 3,5-diglucosides, quercetin, myricetin, and kaempferol glycosides.