Hox genes are master developmental genes that control the identity of different structures and organs along the principal anterior-posterior axis of animals, as well as secondary axes such as the limbs in tetrapods. Two striking properties of Hox genes expression patterns are temporal and spatial colinearity, which are thought to be crucial for the correct specification of eutmetazoan body plans. However, little is known about Hox genes, clusters and their functions in agnathans or cyclostomes (lampreys and hagfishes), the sister group of gnathostomes or jawed vertebrates (i.e. sharks, fishes and tetrapods) and thus in key phylogenetic position to understand the last common ancestor of vertebrates. Here, we present a reference transcriptome of the Japanese inshore hagfish, Eptatretus burgeri, a rare specimen whose embryos are extremely difficult to obtain either in captivity or in natural conditions. We have systematically screened the hagfish transcriptome for Hox genes, and a hagfish BAC library for Hox clusters, finding a total of 40 Hox genes, with up to 6 Hox4 paralogues ( indicative of the presence of up to 6 putative Hox clusters) and a striking phenomenon of somatic differential lost of Hox genes: at least 2 Hox genes are lost in some blood cell types. We have also studied the behavior of Hox gene expression during development in the hagfish and lamprey and compare it with that of gnathostomes (using shark), and found out that colinearity is not that well defined in the hagfish as it is in other vertebrates. Our results might help to understand the big morphological disparities between cyclostomes and gnathostomes, since the regulation of Hox genes seem to be different between the two groups.