The oldest known fossil penguin species is Waimanu manneringi, which lived in the early Paleocene epoch of New Zealand, or about 62 mya (Slack et al. 2006). While they were not as well adapted to aquatic life as modern penguins, Waimanu were generally loon-like birds but already flightless, with short wings adapted for deep diving. They swam on the surface using mainly their feet, but the wings were - as opposed to most other diving birds, living and extinct - already adapting to underwater locomotion.

Perudyptes from northern Peru was dated to 42 mya. An unnamed fossil from Argentina proves that by the Bartonian (Middle Eocene), some 39-38 mya, primitive penguins had spread to South America and were in the process of expanding into Atlantic waters (Clarke et al. 2003).

During the Late Eocene and the Early Oligocene (40-30 mya), some lineages of gigantic penguins existed. Nordenskjoeld's Giant Penguin was the tallest, growing nearly 1.80 meters (6 ft) tall. Found in New Zealand and the Antarctic.

During the Late Eocene and the Early Oligocene (40-30 mya), some lineages of gigantic penguins existed. The New Zealand Giant Penguin was probably the heaviest, weighing 80 kg or more. It was found in New Zealand.

and Eudyptula contain species with a mostly subantarctic distribution centered on South America; some, however, range quite far northwards. They all lack carotenoid coloration, and the former genus has a conspicuous banded head pattern; they are unique among living penguins in nesting in burrows. This group probably radiated eastwards with the Antarctic Circumpolar Current out of the ancestral range of modern penguins throughout the Chattian (Late Oligocene), starting approximately 28 mya (Baker et al. 2006). While the two genera separated during this time, the present-day diversity is the result of a Pliocene radiation, taking place some 4-2 mya (Baker et al. 2006).

It is most interesting to note that the geographical and temporal pattern or spheniscine evolution corresponds closely to two episodes of global cooling documented in the paleoclimatic record (Baker et al. 2006). The emergence of the subantarctic lineage at the end of the Bartonian corresponds with the onset of the slow period of cooling that eventually led to the ice ages some 35 million years later. With habitat on the Antarctic coasts declining, by the Priabonian more hospitable conditions for most penguins existed in the subantarctic regions rather than in Antarctica itself. Notably, the cold Antarctic Circumpolar Current also started as a continuous circumpolar flow only around 30 mya, on the one hand forcing the Antarctic cooling, and on the other facilitating the eastward expansion of Spheniscus to South America and eventually beyond (Baker et al. 2006).

Pygoscelis contains species with a fairly simple black-and-white head pattern; their distribution is intermediate, centered on Antarctic coasts but extending somewhat northwards from there. In external morphology, these apparently still resemble the common ancestor of the Spheniscinae, as Aptenodytes' autapomorphies are in most cases fairly pronounced adaptations related to that genus' extreme habitat conditions. As the former genus, Pygoscelis seems to have diverged during the Bartonian[8], but the range expansion and radiation which led to the present-day diversity probably did not occur until much later, around the Burdigalian stage of the Early Miocene, roughly 20-15 mya (Baker et al. 2006).

The genus Aptenodytes appears to be the basalmost divergence among living penguins; they have bright yellow-orange neck, breast, and bill patches, incubate by placing their eggs on their feet, and when they hatch, they are almost naked. This genus has a distribution centered on the Antarctic coasts and barely extends to some subantarctic islands today.

The origin of the Spheniscinae lies probably in the latest Paleogene, and geographically it must have been much the same as the general area in which the order evolved: the oceans between the Australia-New Zealand region and the Antarctic (Baker et al. 2006). Presumedly diverging from other penguins around 40 mya (Baker et al. 2006), it seems that the Spheniscinae were for quite some time limited to their ancestral area, as the well-researched deposits of the Antarctic Peninsula and Patagonia have not yielded Paleogene fossils of the subfamily. Also, the earliest spheniscine lineages are those with the most southern distribution.

The early Neogene saw the emergence of yet another morphotype in the same area, the similarly-sized but more gracile Palaeospheniscinae, as well as the radiation which gave rise to the penguin biodiversity of our time.

A new lineage, the Paraptenodytes which includes smaller but decidedly stout-legged forms, had already arisen in southernmost South America by that time.

The oldest well-described giant penguin, the 5-foot-tall Icadyptes salasi, actually occurred as far north as northern Peru about 36 mya.