The wild relatives of crop plants are sources of useful genes, but such genes transferred to agricultural crops are often associated with deleterious traits. Because most of the recombination and the disease resistance genes are localized towards the ends of wheat chromosomes, cryptic terminal alien introgressions with leaf rust and stripe rust resistance genes transferred from Aegilops geniculata (U^gM^g) and Ae. triuncialis (U^tC^t) into common wheat were detected using distally mapped molecular markers. Cryptic wheat-alien introgressions with rust resistance were identified using cytological and molecular mapping methodologies combined with selection of the primary recombinants for visual agronomic performance. A wheat-Ae. geniculata alien introgression with the new leaf rust and stripe rust resistance genes, Lr57 and Yr40, respectively, was transferred through induced homoeologous pairing effect of the PhI gene. The alien segment in line T5DL·5DS-5M^gS(0.95) was less than 3.5% of chromosome arm 5DS. Genetic analysis and genomic targeted mapping of wheat-Ae. geniculata introgression using wheat ESTs and synteny with rice suggested that the alien segment with Lr57 and Yr40 genes is less than 3.3 cM in genetic length and spans less than four overlapping BAC/PAC clones of the syntenic rice chromosome arm 12L. Another small alien introgression with the new leaf rust resistance gene Lr58 was transferred from Ae. triuncialis by direct transfer and the introgression in T2BS·2BL-2^tL(0.95) was less than 5% of the chromosome arm 2BL of wheat. Transfer, identification and molecular mapping of the cytologically undetectable primary recombinants with cryptic wheat-alien introgressions suggested that it is feasible to transfer small alien segments with disease resistance genes without the usual linkage drag.