How species originate and how communities of species assemble are among the most intriguing questions in biology, and colonisation is a key element to understand them. Using two island scenarios and applying molecular tools, this thesis looks within species to investigate the themes of colonisation (both island colonisation and European continental recolonisation) and diversification processes in invertebrates. The aim was to address three gaps in our understanding about island colonisation, speciation and the assembly of biota. In the Canary Islands, an oceanic island system, the gaps addressed were: (i) the possibility that genomic admixture among multiple founding lineages has featured in the diversification of a very species rich coleopteran genus; and (ii) the lack of information regarding the colonisation history and dynamics of the small arthropod soil dwelling fauna. In Great Britain, a continental island system, the gap addressed was the under-explored possibility that the UK was not completely defaunated during glaciations, then recolonised from external sources, but that a more complex pattern, involving persistence within small cryptic refugia, may have featured in the history of its invertebrate soil dwelling fauna. I reveal two instances of shared mtDNA variation among weevil species from different Canarian islands for which I was able to dismiss explanations of incomplete lineage sorting and reveal a history of colonisation and speciation involving genetic admixture (first gap). I characterise Collembola evolutionary diversity within Tenerife and the distribution of lineage colonisation times, and reveal this fauna to be represented by a mosaic of very old lineages and a large number of very recently arrived lineages (second gap). Finally, I reveal signatures of survival and persistence of the Collembola fauna through the last Pleistocene glaciation in Great Britain (third gap). How these results fit into a broader evolutionary and conservation context as well as future directions are discussed.