Antigen B (AgB) is an excretory-secretory product of larval stage of Echinococcus granulosus. This antigen is abundantly secreted by larval stage of the worm. AgB is encoded by a multigene family and is suggested to be involved in evasion of host immune system. During the present study a total of 110 animal isolates of E. granulosus has been screened by mutation scan screening. A total of 14 conformers were detected on the basis of single strand banding profile of 129 bp fragment of AgB1 subunit. Analysis of sequence information of 14 conformers could cluster the isolates into two different group viz. buffalo- cattle and sheep-goat cluster. Conceptual amino acid sequence information of two clusters could be differentiated in terms of MHCII binding propensity of agretope and B-cell epitope region. This type of analysis of clustering of animal isolates on the basis of binding propensity towards different MHC antigens and B-cell linear epitope is the example of its own kind. Positive Tajima's D value indicated that, AgB1 is under balancing selection pressure which might be considered as heterogeneous selection pressure exerted by the host. © Springer Science+Business Media B.V. 2009.