Throughout the Common Era, Japan's population saw relatively steady growth between each century. Failed invasions and distance from Asia's mainland meant that Japan was unaffected by many pandemics, primarily bubonic plague, therefore its development was not drastically impeded in the same way as areas such as China or Europe. Additionally, religious practices meant that hygiene was prioritized much more in Japan than in other regions, and dietary customs saw lower rates of meat consumption and regular boiling of water in meals or tea; both of these factors contributed to lower rates of infection for many parasitic or water-borne diseases. Fewer international conflicts and domestic stability also saw lower mortality in this regard, and Japan was an considered an outlier by Asian standards, as some shifting trends associated with the demographic transition (such as lower child mortality and fertility) began taking place in the 17th century; much earlier time than anywhere else in the world. Yet the most significant changes came in the 20th century, as Japan's advanced healthcare and sanitation systems saw drastic reductions in mortality. Challenges Japan's isolation meant that, when pandemics did arrive, the population had less protection and viruses could have higher mortality rates; smallpox has been cited as the deadliest of these pandemics, although increased international contact in the late 19th century brought new viruses, and population growth slowed. Earlier isolation also meant that crop failure or food shortages could leave large sections of the population vulnerable, and, as mentioned, the Japanese diet contained relatively little meat, therefore there was a higher reliance on crops and vegetables. It is believed that the shortage of arable land and the acidity of the soil due to volcanic activity meant that agriculture was more challenging in Japan than on the Asian mainland. For most of history, paddy fields were the most efficient source of food production in Japan, but the challenging nature of this form of agriculture and changes in employment trends gradually led to an increased reliance in imported crops. Post-Sakoku Japan Distance from the Asian mainland was not the only reason for Japan's isolation; from 1603 to 1853, under the Tokugawa shogunate, international trade was restricted, migration abroad was forbidden, and most foreign interaction was centered around Nagasaki. American neo-imperialism then forced Japan to open trade with the west, and Japan became an imperial power by the early-1900s. Japanese expansion began with a series of military victories against China and Russia at the turn of the century, and the annexation of Taiwan, Korea, and Manchuria by the 1930s, before things escalated further during its invasion of China and the Second World War. Despite its involvement in so many wars, the majority of conflicts involving Japan were overseas, therefore civilian casualties were much lower than those suffered by other Asian countries during this time. After Japan's defeat in 1945, its imperial ambitions were abandoned, it developed strong economic ties with the West, and had the fastest economic growth of any industrial country in the post-WWII period. Today, Japan is one of the most demographically advanced countries in the world, with the highest life expectancy in most years. However, its population has been in a steady decline for over a decade, and low fertility and an over-aged society are considered some of the biggest challenges to Japanese society today.

In 1800, the population of Japan was just over 30 million, a figure which would grow by just two million in the first half of the 19th century. However, with the fall of the Tokugawa shogunate and the restoration of the emperor in the Meiji Restoration of 1868, Japan would begin transforming from an isolated feudal island, to a modernized empire built on Western models. The Meiji period would see a rapid rise in the population of Japan, as industrialization and advancements in healthcare lead to a significant reduction in child mortality rates, while the creation overseas colonies would lead to a strong economic boom. However, this growth would slow beginning in 1937, as Japan entered a prolonged war with the Republic of China, which later grew into a major theater of the Second World War. The war was eventually brought to Japan's home front, with the escalation of Allied air raids on Japanese urban centers from 1944 onwards (Tokyo was the most-bombed city of the Second World War). By the war's end in 1945 and the subsequent occupation of the island by the Allied military, Japan had suffered over two and a half million military fatalities, and over one million civilian deaths.

The population figures of Japan were quick to recover, as the post-war “economic miracle” would see an unprecedented expansion of the Japanese economy, and would lead to the country becoming one of the first fully industrialized nations in East Asia. As living standards rose, the population of Japan would increase from 77 million in 1945, to over 127 million by the end of the century. However, growth would begin to slow in the late 1980s, as birth rates and migration rates fell, and Japan eventually grew to have one of the oldest populations in the world. The population would peak in 2008 at just over 128 million, but has consistently fallen each year since then, as the fertility rate of the country remains below replacement level (despite government initiatives to counter this) and the country's immigrant population remains relatively stable. The population of Japan is expected to continue its decline in the coming years, and in 2020, it is estimated that approximately 126 million people inhabit the island country.

The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.