Mango (Mangifera indica L.) is mostly distributed in the two eco-geographical regions (Coastal and Rayalaseema) of an Indian state of Andhra Pradesh, where large morphological and genetic diversity has been detected due free pollination among plants. A juicy landrace-specific exploration survey covering the two eco-geographical regions was undertaken during 2008 to identify new juicy landraces of mango with high fruit quality. Following a selective sampling strategy, 20 indigenous landraces of mango were selected according to fruit morphology and their fruit and leaf samples were collected for morpho-physiological and molecular characterization, respectively. Morpho-physiological characterization and evaluation based on fruit characteristics revealed that six landraces viz., DM Acc-3, 4, 7, 15, 17 and 18 were elite with respect to fruit characteristics, which were further characterized for their genetic distinctiveness and relationships with the choicest juicy cultivars of mango in Andhra Pradesh ('Peddarasam', 'Chinnarasam', 'Cherukurasam', 'Panchadarakalasa' and 'Suvarnarekha') at the molecular level, using 109 mango-specific microsatellite markers (SSRs). Jaccard's similarity coefficient ranged from 0.40 to 0.69 signifying wide variability in the landraces of mango to an extent of 31-60%, offering ample scope for selection. Of the 109 SSR markers validated, 57 were polymorphic, of which 10 were highly polymorphic. Diversity was high among 11 genotypes with a total number of 198 alleles displayed. Microsatellite SSR-84 was able to differentiate and/or identify all of the 11 genotypes under study. UPGMA cluster analysis revealed that the six elite landraces viz., DM Acc-3, 4, 7, 15, 17 and 18 clustered according to their geographical origin. Being horticulturally superior and genetically distinct, these six land races can be clonally selected for further testing and multiplication for commercial exploitation.