Kin selection theories have generally assumed that maternally inherited genes and paternally inherited genes are expressed identically. Recent studies of genomic imprinting showed that matrigenes and patrigenes can be differentially marked and these marks lead to differential expression. Haig's kinship theory provided a theoretical framework that can explain genomic imprinting as a result of within-genome conflict over the offspring’s trait. It has been argued that the best novel contexts for testing this theory are supplied by the haplodiploid social insects. Here we show that termites, i.e., the diplodiploid eusocial insects, also provide ideal tests of Haig's kinship theory. We developed a multilocus imprinting model to examine the potential impact of genomic imprinting on genes that determine the carrier female’s propensity to develop into neotenic queens. This model explains the mechanism of AQS (asexual queen succession), where only parthenogenetically produced daughters are able to circumvent the inhibitory queen pheromone and differentiate into neotenic queens. Because inbreeding depression due to king-daughter mating comes at a colony-level cost, the conflict between matrigenes and patrigenes favors maternal imprinting, but not paternal imprinting.