Most benthic marine invertebrates have complex life cycles which include motile larvae and more or less immobile adult stages. The colonization of surfaces by marine invertebrate larvae is a fundamental process that governs distribution patterns and biodiversity of marine invertebrates. The transition between these life stages is linked to the choice for appropriate habitats via cues for larval settlement and metamorphosis. While marine biofilms have long been recognized as a cue source for larval settlement of phylogenetically diverse invertebrates, the list of chemically identified settlement compounds is surprisingly short. In this chapter we review the current approach to identify larval settlement cues and discuss the difficulties in differentiating between settlement cues associated with animals or plants and those originating from prokaryotic microbes associated with living surfaces. We further argue for the need to integrate larval ecology, environmental microbiology, analytical chemistry and surface physics to measure the natural distribution and abundance of larval settlement cues and judge their ecological relevance and plausibility.