Abstract Many colors and patterns in nature are regulated by the packaging and processing of intracellular pigment-containing organelles within cells. Spanning both molecular and tissue-level spatial scales with chemical and physical (structural) elements of coloration, pigment organelles represent an important but largely understudied feature of every biological system capable of coloration. Although vertebrate melanosomes have historically been the best-known and most studied pigment organelle, recent reports suggest a surge in studies focusing on other pigment organelles producing a variety of non-melanic pigments, optic crystals and structural colors through their geometric arrangement. In this issue, we showcase the importance of these integrative and comparative studies and discuss their results which aid in our understanding of organelle form and function in their native environment. Specifically, we highlight how pigment organelles can be studied at different scales of organization, across multiple species in biology, and with an interdisciplinary approach to better understand the biological and chemical mechanisms underlying color. This type of comparative approach provides evidence for a common origin and identity of membrane-bound pigment organelles not only in vertebrates, as was originally postulated 40 years ago, but in all animals. This indicates that we have much to gain by studying a variety of pigment organelles, as the specific biological context may provide important and unique insights into various aspects of its life. We conclude by highlighting some barriers to this research and discussing strategies to overcome them through a discussion of future directions for pigment organelle research.