The microbiome-behaviour relationship may be especially relevant for fish, due to their diverse evolutionary history and potential applications for farming and conservation. Yet, there is limited research of the interaction between gut microbiome and behaviour in fish, apart from using zebrafish as a model for human applications. We manipulated the rearing environment and diet of fish from two highly inbred strains of the self-fertilising mangrove killifish (Kryptolebias marmoratus) and assessed their effects on the gut microbiome (based on 16S rRNA sequencing) and the potential interactions with behaviour (based on a novel object test).