<p>Studies investigating social evolution often focus on species that are obligately eusocial, where presumably all of the adaptive genetic changes associated with sociality have already been completed. To fully understand eusociality, we must study species with facultative social behaviour. The small carpenter bee <i>Ceratina calcarata</i> is an ideal model for studying the genetics and molecular biology of eusocial evolution as it can exhibit both subsocial behaviour with parental care and social behaviour facilitated by the altruistic dwarf eldest daughter. Here, we sequenced the genomes of subsocial and social <i>C. calcarata</i> to identify mutations and genes associated with social behaviour and used these data to test several hypotheses related to the evolution of eusociality. Many single nucleotide polymorphisms that had high levels of genetic differentiation (F_st) between social and subsocial <i>C. calcarata</i> were in or near genes or regions important for regulating gene expression. These results are consistent with the Genetic Toolkit Hypothesis of eusocial evolution. Our findings suggest that the low behavioural complexity observed in <i>C. calcarata</i> may involve modulation of existing regulatory genes and gene networks to generate phenotypes associated with social behaviour.</p>