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A study was conducted to investigate the evolutionary relationships of <i>Macrotermes subhyalinus</i> from Oman, in the southeastern part of the Arabian Peninsula. Sequences of the mitochondrial <i>COI</i> and the nuclear large-subunit ribosomal RNA (LSU rRNA, <i>28S</i>) genes were used to investigate the populations of <i>M. subhyalinus</i> across their distribution in Oman to determine their relationships with other <i>Macrotermes</i> species. Our findings indicate that <i>M. subhyalinus</i> in Oman is a member of an East African clade, distinct from those in West Africa. Analyses of the <i>COI</i> showed that there is base composition bias among the taxa (non-stationarity) that has not been considered in earlier studies. We provide the first report of pseudogene copies of <i>28S</i> in <i>M. subhyalinus</i> that are differentially amplified.