Distant hybridization has been widely used as important tool of chromosome manipulation for wheat improvement to support the world’s ever-increasing population. Accurately identifying exogenous chromosome(s) or chromosome segments or genes is very important after alien genetic material has been introduced successfully into wheat, but remains challenging. Here, we report the establishment of a set of high-resolution wheat arrays for tracing alien genetic information through genotyping by target sequencing system and liquid chip, including GenoBaits®WheatplusEE (Triticum aestivum-Thinopyrum elongatum liquid chip), GenoBaits®WheatplusRR (Triticum aestivum-Secale cereale liquid chip), GenoBaits®WheatplusPh (Triticum aestivum-Psathyrostachys huashanica liquid chip), and GenoBaits®WheatplusSt (Triticum aestivum-Pseudoroegneria spicata liquid chip). A total of 90000 capture probes derived from two species were integrated into one chip, including 10000 and 80000 within wheat and corresponding distant species. The capture probes were designed to be preferentially located in genes and evenly distributed across the genome, supporting the development a roadmap guiding each alien genes. The genetic information for both wheat and distant species can be generated by target sequencing the sample only once. These liquid chips can be employed in distant hybridization germplasm identification (e.g. alien substitution, addition, or translocation lines), alien gene cloning, and wheat variety or materials protection. We expect GenoBaits®Wheatplus* to become a popular tool that empowers future exploring the wild germplasm for wheat improvement.