Polyploidy is a common mode of evolution in flowering plants. Both the natural tetraploid Thinopyrum elongatum and the diploid one from the same population showed a diploid-like pairing in meiosis. However, the debate on the chromosome composition and origin of the tetraploid Th. elongatum was going on. Here we obtained the induced tetraploid Th. elongatum and found that the induced and natural tetraploids are morphologically close, except for slower development and lower seed setting. By using probes developed from single chromosome microdissection and Fosmid library, obvious differentiations were discovered between two chromosome sets (E1 and E2) of the natural tetraploid Th. elongatum but not the induced one. Interestingly, hybrid F1 derived from the two different wheat-tetraploid Th. elongatum amphiploids 8802 and 8803 produced seeds well. More importantly, the analysis on meiosis in F2 individuals revealed that chromosomes from E1 and E2 could pair well on the durum wheat background with the presence of Ph1. No chromosome set differentiation on FISH level was discovered from the S1 to S4 generations in the induced one. In metaphase of the meiosis first division in the natural tetraploid, more pairings were bivalents and fewer quadrivalents with ratio of 13.94 II+0.03 IV (n=31). Chromosome pairing configuration in the induced tetraploid is 13.05 II+0.47 IV (n=19), with the quadrivalent ratio only slightly higher than the ratio in the natural tetraploid. Therefore, the natural tetraploid Th. elongatum was of autoploid origin and the induced tetraploid Th. elongatum evolutionarily underwent rapid diploidization in the low generation.