This study investigated the molecular characteristics and amylopectin unit and internal chain profiles of two yellow pea starches with significantly different pasting properties, before and after they were chemically gelatinized with 13M lithium chloride solution to separate the periphery and the core of their starch granules. The sample with a lower peak, final and setback viscosities but a higher pasting temperature was labeled P1, while P2 had opposite pasting properties. Prior to chemical gelatinization, large starch granules (> 20 µm) were separated from the starches to ensure uniform chemical gelatinization. After physically separating the gelatinized portion (about 45%) of the granules, amylopectin was fractionated from all three fractions i.e. native large granules (LG), remaining granules (RG) and the gelatinized portion of the granules (GP). RG represented the core while GP represented the periphery of the granules. Granule size distribution, iodine binding, molecular size distribution, thermal properties, percent crystallinity as well as the unit and internal chain profiles as ,-limit dextrins of fractionated amylopectin were determined. Granules from both samples had a unimodal distribution with sizes averaging 25.44 and 26.51 µm for P1 and P2 respectively. Starches exhibited the typical C-type crystal allomorphs with amylose contents ranging between 33.27 and 28.37%. The two samples exhibited similar unit chain profiles, but significant differences were observed in their internal chains. Extracted amylopectin samples were observed to have super long chains with average chain lengths of 18.75 and 19.24 glucose units for P1 and P2 respectively. P1 with lower pasting viscosities had significantly shorter average chains and internal chains (4.95 glucose units) and P2 with lower gelatinization temperature had less of crystalline A-chains (Acrystal). The two samples had significantly different internal chain profiles that could explain the differences in their pasting profiles. The LG of P1 required 300 min to gelatinize to about 45% of the granule while P2 took 190 min. The results revealed that amylose was evenly distributed in P1 but more concentrated at the periphery of granules in P2. The periphery of granules had more short chain amylose than in the core for both samples. The short chain length (SCL) and long B-chains of ,-limit dextrins (BLLD) were longer at the core where more of B-allomorphs are known to be distributed in both samples. Fingerprint A-chains (Afp), short B-chains (BS) and B-chains were more concentrated at the periphery than at the core.