Camels are dromedaries found in extreme desert environments of Africa and Asia with adaptations to arid conditions of temperatures exceeding 40°C, water losses greater than 25% of total body weight, and the ability to survive up to 14 d without water. Camels are important as beasts of burden for transport and as sources of meat, milk and wool in many desert countries. Therefore, camel could be very useful in the weather extremes precipitated by global climate change. Recent sequences of camelidae genomes [wild bactrian camel (Camelus bactrianus ferus), bactrian camel (Camelus bactrianus), dromedary (Camelus dromedaries) and alpaca (Vicugna pacos)] provides the opportunity to better understand the genomic architecture of this unique group of animals. CpG island (CGIs) sequence patterns in complex genomes typically consists of high-frequency of CpG dinucleoetides associated with promoter regions of about 70% of all genes, found in almost all housekeeping genes and in about half of tissue-specific genes. CGIs play important roles in the regulation of gene expression including X-chromosome inactivation, imprinting, silencing of intragenic parasites and are extensively linked to the epigenetic causes of cancer. We used newly available genomic sequence to perform comparative large-scale whole-genome analysis of CGIs for the first time in Camelidae using 5 different CGI detection algorithms. These algorithms detected different numbers of CGIs, CGI density and CGI length distribution in Camelidae. All algorithms agreed on the alpaca genome as having the largest number of CGIs, CGI density and average length of CGIs. When compared with other mammalian genomes of human, mouse, dog, horse and cow, CGIs features in cow genome was the most similar with camelid genomes. These results contribute to better understanding of the evolutionary genetics of camelid genomes in comparison with other livestock species. Further analysis of camelid genomes may shed more light on molecular origins and mechanisms of heat adaptation in these extreme heat-adapted animals.