The objectives of this study were investigated the variations of agronomic traits, developmental progress, and genotype makeup in Taiwan wild rice. The materials were collected from germplasm nursery of Taiwan Agriculture and Research Institute. All of the 48 tested survival lines could be divided to three different plant types by appearance phenotype. Type Ⅰ was similar to Type Ⅲ except the color of leaf sheath. Type Ⅰ had purple brown sheath and Type Ⅲ showed pale green sheath, and they had a smaller angle between tillers and ground. The phenotype of Type Ⅱ was similar to that of culture varieties and angle between tillers and ground was near 90 degree. The color of leaf and leaf sheath of type Ⅱ lines were green. The heading day of wild rice in Taiwan was longer than that of culture varieties. Average days from transplant to heading of wild rice in Taiwan was 132. Among the three types, Type Ⅲ had the stronger growth vigor in the traits of plant height, tiller number per plant and leaf number of main stem. The variation of spikelet fertility was the largest among the components of yield. A total of 10 DNA simple sequence repeat (SSR) primer pairs were selected to detect genotype polymorphisms among 48 Taiwan wild rice lines, 9 culture varieties, and 7 wild rice accession lines from IRRI. Ten SSR primers amplified a total of 38 polymorphic bands. The average number of alleles per SSR locus was 3.8 with a range 2 to 6. UPGMA cluster analysis proposed that the 64 rice materials could be divided into 6 groups. Although almost all of Taiwan wild rice lines were clustered into the same group, considerable DNA polymorphism was found among these lines. The present results revealed that Taiwan wild rice may be a high heterogenous population with respect to agronomic traits and genetic background. This population also showed some Japonica-like traits, suggesting introgression might occur during long period of coexistence with other cultivars. Most of modern crop cultivars are domestication from their wild ancestors. Oryza sativa L., the most widely cultivated and important rice species in the world is recognized to be evolved from Oryza rufipogon. And Oryza rufipogon is also an important genetic resource for the breeding improvement of the present rice cultivars. Because of the civilization and urbanization, more and more wild species have gradually lost their habitats and have been becoming extinct. In Taiwan wild rice species was first discovered around Taoyuan and Shinchu areas, but because of the reasons mentioned above, they have become endangered species. So far, only limited scientists had done preliminary researches on Taiwan wild rice, and very few knowledge about the agronomic and quality traits of Taiwan wild rice have been documented. This study was aimed to make serial investigations on morphological characteristics, amylose content, crude-protein content, and storage protein of grains of Taiwan wild rice. In addition, protein electrophoresis based proteomic approach was utilized to study the expression specialty of storage proteins in the wild rice. In grain morphological traits, different grain colors from gray black to light yellow were found within wild rice population. The long grain shape of Taiwan wild rice was found to be closed to that of modern Indica type cultivars. The modern cultivar-like grain morphological traits appeared within Taiwan rice population might be due to the high cross-pollination rate of the wild rice and the long coexistence between the wild rice and modern cultivars in the field. In grain chemical properties, apparent variations in amylase, crude protein content, and storage protein contents were found in Taiwan wild rice population. Amylose contents of Taiwan wild rice lines were ranged between 12.3% and 28.4%. Crude protein content varied between 9.64% and 16.64%. The low amylase and high protein contents suggest that Taiwan wild rice are prominent breeding resources for the improvement of protein or amylase content of modern rice cultivars. Regarding expressions of grain storage proteins revealed by 1D and 2D electrophoresis, Taiwan wild rice accumulated higher amount of glutelins and prolamines than modern cultivars. Expression patterns of urea soluble proteins on 1D gel, mainly glutelins and prolamins, were closer to that of modern cultivars. Differential expressions of some proteins were observed within the wild rice population. In addition, profiles of 2D gels showed polymorphism in the expressions of glutelins and prolamines within the wild rice population. The present results suggest that Taiwan wild rice is a heterogeneous population which may harbor a certain number of traits/genes from cultivars. Results of the current study may offer valuable information for both maintenance and utilization of Taiwan wild rice.