Development of a complete wheat-Thinopyrum junceiforme amphiploid facilitated identification of resistance to multiple pests and abiotic stress derived from the wild species and shed new light on its genome composition. Wheat production is facing numerous challenges from biotic and abiotic stresses. Alien gene transfer has been an effective approach for wheat germplasm enhancement. Thinopyrum junceiforme, also known as sea wheatgrass (SWG), is a distant relative of wheat and a relatively untapped source for wheat improvement. In the present study, we developed a complete amphiploid, 13G819, between emmer wheat and SWG for the first time. Analysis of the chromosome constitution of the wheat-SWG amphiploid by multiple-color genomic in situ hybridization indicated that SWG is an allotetraploid with its J1 genome closely related to Th. bessarabicum and Th. elongatum, and its J2 genome was derived from an unknown source. Two SWG-derived perennial wheat lines, 14F3516 and 14F3536, are partial amphiploids and carry 13 SWG chromosomes of mixed J1 and J2 genome composition, suggesting cytological instability. We challenged the amphiploid 13G819 with various abiotic and biotic stress treatments together with its emmer wheat parent. Compared to its emmer wheat parent, the amphiploid showed high tolerance to waterlogging, manganese toxicity and salinity, low nitrogen and possibly to heat as well. The amphiploid 13G819 is also highly resistant to the wheat streak mosaic virus (temperature insensitive) and Fusarium head blight. All three amphiploids had solid stems, which confer resistance to wheat stem sawflies. All these traits make SWG an excellent source for improving wheat resistance to diseases and insects and tolerance to abiotic stress.