Common wheat has complex genome composition of homoeologous hexaploid (AABBDD, 2n = 6x = 42) and each homoeologous genome has high similarity. Due to these complexity, wheat genome study is a large challenge to researchers for genomic and genetic study. We analyzed expressions of individual wheat genome and rye genome specific transcripts using custom array with 2BS.2RL wheat-rye translcoation. Genomic probes were synthesized within each diploid progenitors (AA, BB, DD, 2n = 14, respectively) of wheat, common wheat, and rye (RR, 2n = 14). Total RNA isolated from seedlings of T. urartu, Ae. speltoides, Ae. squarrosa, ‘Chinese Spring’, ‘Chaupon’, and 2BS.2RL were hybridized on arrays. Each homoeologous gene differentially expressed in hexaploid wheat and rye were identified on the custom array and the transcripts were clustered based on hybridization values. qRT-PCR was performed to verify the custom array result with a set of five genes by highly replicated experiments (three biological and three technical replications). The qRT-PCR results demonstrated genome specific expression of five genes in sympathy with array results. Here we provide information of each individual genome specific transcripts and it will we a useful data to study complex wheat genome compositions.