The maize landraces in the North East Himalayan (NEH) region in India, especially in the Sikkim state, are morphologically highly diverse. The present study provides details of phenotypic and molecular characterization of a set of 48 selected maize landrace accessions, including the 'Sikkim Primitives' which have a unique habit of prolificacy (5-9 ears on a single stalk). Multi-location phenotypic evaluation of these 48 accessions revealed significant genetic variability for grain yield and its components, leading to identification of several promising accessions. Cluster analysis and PCA using nine morpho-agronomic characters clearly separated 'Sikkim Primitives' from the rest of the accessions. PCA revealed two principal components describing 90% of the total variation, with hundred kernel weight, ear length, ear diameter, number of kernels per ear and flowering behaviour forming the most discriminatory traits. The accessions were genotyped using 42 microsatellite or simple sequence repeat (SSR) markers using a 'population bulk DNA fingerprinting strategy', with allele resolution using an automated DNA Sequencer. The study revealed a high mean number of alleles per SSR locus (13.0) and high Polymorphism Information Content (PIC) value of 0.60. The analysis also led to identification of 163 private/unique alleles, differentiating 44 out of 48 accessions. Six highly frequent SSR alleles were detected at different loci (phi014, phi062, phi090, umc1266, umc1367 and umc2250) with individual frequencies >/=0.75. Some of these SSR loci were reported to tag specific genes/QTL for some important traits, indicating that chromosomal regions harboring these SSR alleles were not selectively neutral. Cluster analysis using Rogers' genetic distance also revealed distinct genetic identity of the 'Sikkim Primitives' from the rest of the accessions in India, including Sikkim. Mantel's test revealed significant and positive correlation between the phenotypic and molecular genetic dissimilarity matrices. The study was the first to portray the patterns of phenotypic and molecular diversity in the maize landraces from the NEH region in India.