Synchronized peripheral blood lymphocytes from both river buffalo (BBU) and sheep (OAR) were treated for late incorporation of both BrdU and H-33258 to obtain R-banded preparations to be used for FISH-mapping. Ovine BAC-clones were hybridized for three days on slides pre-exposed to UV light after H-33258 staining. The following loci were mapped: <i>GPR103</i> (BBU7q13, OAR6q13), <i>TRAM1L1</i>(OAR6q13dist), <i>PPP3CA</i> (BBU7q21, OAR6q15), <i>SNCA</i> (OAR6q17), <i>PPARGC1A</i>(BBU7q23, OAR6q17), <i>UGDH</i> (BBU7q25prox, OAR6q22prox), <i>KDR</i> (BBU7q27, OAR6q22), <i>CNOT6L</i> (BBU7q32prox, OAR6q32prox), <i>NUP54</i> (BBU7q32, BBU6q32), <i>DMP1</i> (BBU7q34dist-q36prox, OAR6q34dist-q36prox), <i>QDPR</i> (BBU7q36, OAR6q36). All loci mapped in homoeologous chromosomes and chromosome bands of the two species and their locations are in agreement with the previous RH-mapping performed on BBU7 with some difference in the distal region of BBU7. However, the present cytogenetic map better anchors the RH-map on specific river buffalo chromosome bands. In addition, eleven loci were assigned for the first time in sheep to OAR6, noticeably extending the cytogenetic map on this important chromosome which encodes caseins. Two loci <i>(TRAM1L1</i> and <i>SNCA)</i> mapped in sheep were unmapped in river buffalo in three different FISH experiments. Comparisons between integrated cytogenetic maps of BBU7/OAR6 (and BTA6) with human chromosome 4 (HSA4) revealed complex chromosome rearrangements differentiating these chromosomes.