North- Eastern parts of India fall under the Eastern Himalayan region and it is a diversity hotspot of many crops, including maize. Maize is an important traditional cereal crop grown in hill ecology of the region mainly for food, fodder and feed. To tap the potentiality of maize genetic resources in crop improvement programmes, assessment of genetic diversity is a basic requirement. Hence, in the present study, assessment of genetic diversity in thirty early generation maize inbreds developed from different germplasm of NE India was taken up using genome wide distributed fifty two microsatellite markers. The marker analysis revealed a large variation with a total of 189 alleles with an average of 3.63 alleles per marker locus. The allele size ranged from 50 bp ( phi 036 ) to 295 bp ( p 101049 ) which revealed a high level of genetic diversity among the loci. The PIC value ranged from 0.17 ( umc 1622 ) to 0.76 ( umc 1153 ) with an average value of 0.49. The value of expected Heterozygosity (H Exp ) ranged from 0.19 to 0.80 with an average of 0.57, whereas the Observed Heterozygosity (H Obs ) ranged from 0 to 0.89 with a mean of 0.14.The genetic dissimilarity between the genotype pairs ranged from 0.40 to 0.64 with a mean value of 0.57. Cluster analysis resolved the inbreds into three distinct sub-clusters. Similarly, population structure analysis also classified the inbred lines into three-subpopulations. Marker-trait associations showed a total of twelve SSR markers significantly associated with seven agronomic traits. From the present study, wide genetic variability was found among the maize inbreds with high potential to contribute new beneficial and unique alleles in genetic enhancement program of maize in India and particularly, in NE region.