Well-characterized molecular and cytogenetic maps are yet to be established in Japanese quail (JQ) (Coturnix japonica). The aim of the current study was to cytogenetically map and determine linkage of specific genes and gene complexes in JQ through the use of chicken (Gallus gallus domesticus) and turkey (Meleagris gallopavo) genomic DNA probes. Seven BACs and four plasmid clones were used as probes on mitotic metaphase and/or meiotic pachytene stage chromosomes of the three species for the purpose of high-resolution fluorescence in situ hybridization (FISH). The genes and complexes studied included: 5S rDNA, 18S-5.8S-28S rDNA (a.k.a. Nucleolus Organizer Region (NOR)), the Major Histocompatibility Complex (MHC), telomerase RNA (TR) and the telomerase reverse transcriptase (TERT). In addition, the telomeric profile of JQ was investigated by FISH using a TTAGGG-PNA probe. Three NOR loci were identified in JQ, and single loci each for TR, TERT, 5S rDNA and the MHC. The MHC and one NOR locus were linked on the q-arm of a micro-chromosome in JQ, with the NOR interstitially located. We also confirmed physical linkage of the 5s rDNA and the TR gene on an intermediate-sized chromosome in JQ, similar to chicken and turkey. TERT localized to chromosome 2q in JQ and 3q in turkey, which are orthologous to chromosome 2 in chicken. A range of telomeric array sizes were found in JQ including mega-telomeres as in the other poultry species. The cytogenetic profile of JQ was further developed by this study and synteny was identified among the three species.