In this penultimate chapter of the Origin, Darwin ties together three key areas: Morphology, embryology, and rudimentary organs. He wants to support the argument that all species descend from common ancestors. These subjects may seem disconnected at first, but for Darwin, they converge on a single principle: similarity, when properly understood, reflects shared ancestry.
The chapter opens with a discussion of classification systems. Since antiquity, naturalists have grouped organisms based on similarity. Linnaeus formalized this in his Species Plantarum, creating a hierarchy of taxa: From species to genera, families, and beyond. But what do these similarities actually mean? Darwin’s answer is evolutionary: the natural system is not arbitrary but reflects the pattern of descent with modification. Organisms are grouped because they inherited traits from common ancestors. Lineages split over time, and these splits form the nested hierarchy seen in taxonomy. He revisits the tree-like diagram introduced earlier in the book to visualize this branching process.
Crucially, Darwin emphasizes that good classification depends on distinguishing between homology and analogy. Homologous traits are inherited from a shared ancestor; analogous traits arise independently in unrelated lineages due to similar selective pressures. Whales and fish both have streamlined bodies, but this similarity is not due to shared ancestry. It is an adaptation to aquatic life. Therefore, Darwin argues, traits that are functionally important but shaped by specific habits (like swimming) are of little taxonomic value. Instead, those characters less influenced by lifestyle, such as the structure of bones, are more reliable indicators of evolutionary relationships.
One of the most striking kinds of homology, according to Darwin, comes from comparing limbs in vertebrates. The human hand, the wing of a bat, and the flipper of a porpoise all share the same underlying bone structure, modified for different uses. For a creationist, this is inexplicable. Why would a divine designer reuse the same structure for such different purposes? For Darwin, it makes perfect sense: natural selection modified a shared ancestral limb into different forms depending on the needs of the organism.
Darwin extends this argument to serial homology, the repetition of similar structures within a single organism. He points to annelids and arthropods, whose segmented bodies include repeated units, and to plants, whose reproductive organs are often modified leaves. This pattern of repetition and transformation, he argues, is only intelligible in evolutionary terms.
From morphology, Darwin moves to embryology: A field he saw as one of his most important but least appreciated contributions. Embryos, he writes, often reveal affinities between species that are hidden in adult forms. Vertebrate embryos, for example, start out so similar that Agassiz once remarked he could not distinguish whether a particular embryo belonged to a mammal, bird, or reptile. Darwin emphasizes that these early-stage similarities are especially telling because they are not shaped by the needs of the organism. An embryo’s features are less likely to be affected by its environment or behavior. Therefore, they offer a clearer window into ancestry.
He illustrates this with the presence of branchial arches (structures that resemble gill slits) in the embryos of vertebrates, including mammals and birds. These features are vestiges of a fish-like ancestry. They do not serve any function in higher vertebrates but persist during early development as a kind of developmental echo. Darwin also discusses how barnacle larvae resemble those of free-swimming crustaceans. Only later do they develop the specialized features of a sessile adult barnacle. The larval forms reveal their true affinities and evolutionary origins.
Darwin insists that these embryonic similarities are not the result of chance. He argues that evolutionary change tends to occur later in development, preserving early stages across species. New adaptations are more likely to emerge in adulthood, where selection pressures are strongest. That’s why adult forms diverge so much, while embryos remain relatively conserved.
Importantly, Darwin does not accept the popular theory of the time that embryos recapitulate adult stages of their ancestors—an idea later associated with Ernst Haeckel. Instead, he sees the embryo as a shadow of the ancestral form, not a full replay. It is a picture, more or less obscured, of the common parent-form of each great class of animals.
Darwin then turns to rudimentary or vestigial organs: Structures that once had a function but are now reduced or unused. Male mammals have rudimentary mammary glands. Baleen whales develop teeth as embryos, only to resorb them before birth. Some snakes possess tiny, hidden remnants of pelvic bones. These structures, Darwin argues, are vestiges of evolutionary history. They are not adaptive; they exist because natural selection has not fully eliminated them yet. In cases where disuse is sustained over generations, selection may eventually lead to their complete disappearance.
He gives special attention to island birds that have lost the power of flight. In the Galápagos, for instance, the flightless cormorant shows reduced wings, a likely result of disuse in the absence of predators. In such cases, Darwin invokes what he calls the principle of economy: selection favors energy efficiency, and maintaining nonfunctional structures wastes resources. Over time, disused organs shrink, atrophy, and may even vanish.
Finally, Darwin circles back to taxonomy. He argues that the best classification systems will group organisms according to shared ancestry. Rudimentary organs, embryonic traits, and homologous structures are all clues to genealogical relationships. Adaptive features shaped by niche or function are often misleading, because they reflect convergence rather than common origin.
Darwin ends the chapter with a strong assertion: the evidence for common descent from morphology, embryology, and rudimentary organs is so compelling that he would accept it even if it were unsupported by other facts or arguments. These three fields provide independent but converging lines of support for his theory. Together, they reveal the deep, branching structure of life, rooted in common ancestry, shaped by natural selection, and preserved in the shared blueprints of bodies and development.