Biologist Ernst Mayr defined a species as “an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so.” A key event in the origin of many species is the separation of a population with its gene pool (all of the genes in a population at any one time) from other populations of the same species, thereby preventing population interbreeding. With its gene pool isolated, a separate population can follow its own evolutionary course. In the formation of many species, the initial isolation of a population seems to have been a geographic barrier. This mode of evolving new species is called allopatric speciation.

Many factors can isolate a population geographically. A mountain range may emerge and gradually split a population of organisms that can inhabit only lowland lakes, certain fish populations might become isolated in this way. Similarly, a creeping glacier may gradually divide a population, or a land bridge such as the Isthmus of Panama may form and separate the marine life in the ocean waters on either side.

How formidable must a geographic barrier be to keep populations apart? It depends on the ability of the organisms to move across barriers. Birds and coyotes can easily cross mountains and rivers. The passage of wind-blown tree pollen is also not hindered by such barriers, and the seeds of many plants may be carried back and forth on animals In contrast, small rodents may find a deep canyon or a wide river an effective barrier. For example, the Grand Canyon, in the southwestern United States, separate the range of the while-tailed antelope squirrel from that of the closely related Harris’ antelope squirrel. Smaller, with a shorter tail that is white underneath, the white-tailed antelope squirrel inhabits deserts north of the canyon and west of the Colorado River in southern California Hams' antelope squirrel has a more limited range in deserts south of the Grand Canyon.

Geographic isolation creates opportunities for new species to develop, but it does not necessarily lead to new species because speciation occurs only when the gene pool undergoes enough changes to establish reproductive barriers between the isolated population and its parent population. The likelihood of allopatric speciation increases when a population is small as well as isolated, making it more likely than a large population to have its gene pool changed substantially. For example, in less than two million years, small populations of stray animals and plants from the South American mainland that managed to colonize the Galapagos Islands gave rise to all the species that now inhabit the islands.

When oceanic islands are far enough apart to permit populations to evolve in isolation, but close enough to allow occasional dispersions to occur, they are effectively outdoor laboratories of evolution. The Galapagos island chain is one of the world’s greatest showcases of evolution. Each island was born from underwater volcanoes and was gradually covered by organisms derived from strays that rode the ocean currents and winds from other islands and continents. Organisms can also be carried to islands by other organisms, such as sea birds that travel long distances with seeds clinging to their feathers.

The species on the Galapagos Islands today, most of which occur nowhere else, descended from organisms that floated, flew, or were blown over the sea from the South American mainland. For instance, the Galapagos island chain has a total of thirteen species of closely related birds called Galapagos finches. These birds have many similarities but differ in their feeding habits and their beak type, which is correlated with what they eat. Accumulated evidence indicates that all thirteen finch species evolved from a single small population of ancestral birds that colonized one of the islands. Completely isolated on the island after migrating from the mainland, the founder population may have undergone significant changes in its gene pool and become a new species. Later, a few individuals of this new species may have been blown by storms to a neighboring island. Isolated on this second island, the second founder population could have evolved into a second new species, which could later recolonize the island from which its founding population emigrated. Today each Galapagos island has multiple species of finches, with as many as ten on some islands.

生物学家厄恩斯特·迈尔将物种定义为“一个可以互相交配或可能互相交配的群体，但这个群体不能与其它生物交配，即便有交配的机会”。许多物种起源时的一个关键事件是有着自己的基因库的种群（任何时候这个种群的所有基因）与该物种其他种群分离。由于基因库被隔离，各自的种群可以按照自身的进程来进化。在许多物种的形成过程中，最初的种群隔离似乎来自一种地理上的屏障，这种进化新物种的模式被称为异域物种形成。 许多因素可以在地域上隔离一个种群。某些山脉的出现会逐渐分离出一个只能在低洼的湖泊中生活的物种，某些鱼类可能就这样被隔离出来了。类似地，冰川的上升可能会慢慢地将同一个种群分开，或者像巴拿马地峡这样的大陆桥会将海洋生物隔离在大陆桥的两边水域。 多么强大的地理屏障才能将种群分开呢？它取决于生物跨越障碍的能力。鸟类和狼可以轻易越过山川河流。那些通过风来传播花粉的树木也不会受到这些壁垒的阻碍，并且很多植物的种子会被动物搬来搬去。相对来说，一个很深的峡谷或一条宽阔的河流可能是小型啮齿类动物的有效屏障。例如，美国西南部的大峡谷将白尾羚羊松鼠的生活范围以及与其密切相关的哈里斯羚羊松鼠的生活范围隔开。白尾羚羊松鼠体型较小，尾巴很短且下面是白色的，栖息于大峡谷以北、科罗拉多河以西的南加利福尼沙漠地区。哈里斯羚羊松鼠的生活范围比较有限，位于大峡谷以南的沙漠地区。 地理隔离为新物种的进化创造了机会，但这并不一定会形成新物种。因为物种形成只有在基因库发生足够大的变化，被隔离的种群与亲本种群之间出现繁殖障碍（即不能交配繁殖）时才发生。种群的数量比较小且被隔离开来时，比数量大的种群更容易发生基因库的实质变化，也就增加了异域物种形成的可能性。例如，从南美大陆流浪而来，成功移居到加拉帕戈斯群岛的动物和植物小种群，在不到二百万年的时间就进化出了现在岛上存在的所有物种。 当海洋岛屿互相之间的距离比较远，使得种群得以独立进化，但又不至于太远从而使得物种可以在偶然的条件下传播过去时，它们就是有效的户外进化实验室。加拉帕戈斯群岛是世界上最伟大的进化展示窗之一。它的每个岛屿都来自海底火山喷发，岛上逐渐住满了洋流和风从其他岛屿和陆地带来的生物。这些生物也可能是被其他生物带到岛屿上来的，如长途飞来的海鸟羽毛上可能沾有其他植物的种子。 今天生活在加拉帕戈斯群岛的物种，是那些由从南美大陆飘过来、飞过来、或者被风吹过来的物种演变而来的，其中大多数物种是岛上独有的，在其他地方见不到。例如，加拉帕戈斯群岛有十三种联系紧密的鸟都叫加拉帕戈斯雀类。这些鸟类有许多相似之处，但他们的饮食习惯和嘴型（与它们所吃的东西有关）存在不同。已经收集到的证据表明，这十三种雀鸟都是从一个小种群的鸟类祖先进化而来的，这个鸟类的祖先在其中的一个岛栖息繁殖。从大陆迁移来后，它们在岛上完全被隔离开来，最初的种群基因库发生了很大的变化，成为一个新的物种。后来，新物种的小部分可能被风暴吹到了邻近的一个岛。它们在这个岛上再次被隔离开来，这第二个初始种群可能又进化出另一个新物种，而这个新物种之后又可能重新回到它的初始种群来自的那个岛。今天每个加拉帕戈斯岛都有多种雀鸟，有些岛上多达十种。