Microsatellite markers were used to analysed the genetic diveristy and structure of twenty six farmer-selected trees in the valley districts of Manipur, India. Three markers, which displayed high polymoprhic information content (88.9%) and allelic richness ranging between 14 and 16. The number of allele per locus (Na) in the pooled selected population was 5.33, number of private alleles was 0.66 and Shannon Diversity Index (I) was 1.12 Na= 3.67; number , indicating high diversity values. Population wise, highest values were obtained in Imphal West ( of private alleles = 1.33, I= 1.05 Na= 1.67; number of private alleles = 0, I= 0.24 Analysis of molecular variance ) and lowest in Chandel ( ). indicated among groups (12.5%). Structure analysis revealed that much of variability resided within selections (49.5%) and very less selections have originated from two genepools, but with no clear-cut inclination of any selection to either genepool. The results indicate that ample genetic variation existed in the twenty farmer-selected trees and informal selections by farmers do not display any genetic deficiencies. However there is a need for an extensive genetic survey comprising of natural and planted populations across the state to enable more meaningful comparisons.