The purpose of this study was to reveal the change of population structure and genetic diversity of wheat germplasm in the process of regeneration and to provide a scientific basis for the collection and conservation of wheat germplasm resources，so as to conserve and utilize the resources more efficiently． Nine agronomic traits were investigated and 35 pairs of microsatellite markers associated with agronomic traits were used to analyze 6 ac- cessions from three wheat varieties，each of the varieties was stored both in the long-term genebank and the mid-term genebank respectively． Population structure and genetic diversity within wheat accessions composed of 30 individual and between two types of conservation were analyzed by agronomic traits and SSR marker． It showed that ( 1) All of three wheat varieties was heterogeneity accession，genetic heterogeneity among individuals was different at the SSR locus with 57． 14% ，48． 57% and 5． 71% respectively． ( 2) The regeneration wheat accessions ( mid-term gene- bank) displayed similar performance in morphological，only plant height and number of spikelets significantly in- creased in wenquanxiaomai3． ( 3) Allele gene frequencies was significantly different and allele absence was ob- served at eight microsatellite sites which was associated with grain weight，grain yield and heading date，genetic diversity reduced after regeneration． ( 4) The analysis of agronomic traits and molecular markers all showed that there was no significant different between the long-term genebank and the mid-term genebank in diversity． The Gst value of three varieties was 0． 0269，0． 0324 and 0． 0380 respectively，only 2． 69% ，3． 24% and 3． 80% differences existed between accessions from the two types of conservation． It suggested that the danger of the loss of genetic in- tegrity exists after regeneration，300 individual should be maintained at least to ensure the genetic integrity in re- generation．