Common wheat originated from interspecific hybridization of three diploid ancestors followed by spontaneous chromosome doubling. Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The first aim of this study was to characterize the homology between the wheat B genome and the Ae. speltoides S genome. In this study, meiotic pairing for each of the B-S homoeologous pairs was investigated individually. Noticeable homology between chromosomes 1B and 1S was discovered, but not between other homoeologous B-S pairs. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B. The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides was involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. Aegilops speltoides and Thinopyrum elongatum (genome EE), two of diploid relatives of wheat, are considered important sources of novel genes for wheat improvement. However, the development of compensating wheat-alien translocations has been limited by laborious cytological analysis. This study aimed to develop an effective procedure of inducing, recovering, and detecting homoeologous recombination in wheat-alien gene introgression lines. Totally, 112 wheat-Ae. speltoides 2B-2S and 87 wheat-Th. elongatum 2B-2E translocation lines were developed through this procedure. Composite bin maps for chromosome 2B as well as homoeologous chromosomes 2S and 2E were constructed by genotyping the translocations using 90K SNP arrays. In addition, genes for resistance to stem rust, tan spot, and SNB on chromosome 2S were physically mapped and incorporated into the wheat genome. Also, an Ae. speltoides-derived deleterious growth gene was physically mapped to the subtelomeric region of chromosome 2S. In summary, the results of the study led to a large number of 2B-2S and 2B-2E recombinants, physically mapped disease and growth-related genes on chromosome 2S, developed novel molecular markers, and optimized chromosome engineering procedures.