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During the 1950s and 60s, a Dutch priest named Father Theodor Verhoeven lived and worked on Flores at a Catholic Seminary. Verhoeven had a keen interest in archeology and had studied it at university. While living on Flores, he identified dozens of archeological sites and conducted excavations at many of these, including the now famous site of Liang Bua where the "hobbits" of human evolution were discovered (Homo floresiensis). Verhoeven was the first to report and publish that stone tools were found in association with Stegodon remains in central Flores at several sites within the Soa Basin. He even argued that Homo erectus from Java was likely behind making the stone tools found on Flores and may have reached the island around 750,000 years ago. At the time, paleoanthropologists took little notice of Verhoeven's claims or if they did, they discounted them outright.

Almost thirty years later, an Indonesian-Dutch research team uncovered evidence at the Soa Basin which confirmed Verhoeven's original findings. This team even went further by dating some of the stone tools and fossils using paleomagnetism (a method of determining the age of ancient sediments) and showed they were probably around 700,000 years old. These new findings did not become widely known within the paleoanthropological community until additional sediments were dated using a different technique called zircon fission-track analysis. Thus, by the late 1990s more scientists were beginning to accept the possibility that another human species (likely Homo erectus) had crossed the Wallace Line and reached Flores well before our own species, Homo sapiens, had evolved in Africa around 200,000 years ago.

In 2001, an Indonesian-Australian research team began excavations at a large limestone cave located in west central Flores. This cave, known as Liang Bua (which means "cool cave"), was first excavated by Father Verhoeven in 1965. Professor Raden Soejono, the leading archeologist in Indonesia, heard about Liang Bua from Verhoeven and conducted six different excavations there from the late 1970s until 1989. All of this early work at Liang Bua only explored deposits that occurred within the first three meters of the cave floor. These deposits are dated to within the last 10,000 years and contain considerable archeological and faunal evidence of modern human use of the cave, as well as skeletal remains of modern humans. However, in 2001 the new goals were to excavate deeper into the cave's stratigraphy to explore if modern or pre-modern humans were using Liang Bua prior to 10,000 years ago. In September of 2003, they got their answer.

On Saturday, September 6, 2003, Indonesian archeologist Wahyu Saptomo was overseeing the excavation of Sector VII at Liang Bua. Benyamin Tarus, one of the locally hired workers, was excavating the 2 x 2 meter square when all of a sudden the top of a skull began to reveal itself. Six meters beneath the surface of the cave, Wahyu immediately joined Benyamin and the two of them slowly and carefully removed some more sediment from around the top of the skull. Wahyu then asked Indonesian faunal expert Rokus Due Awe to inspect the excavated portion of the skull. Rokus told Wahyu that the skull definitely belonged to a hominin and most likely that of a small child given the size of its braincase. Two days later, the team returned to the site and Thomas Sutikna, the Indonesian archeologist in charge of the excavations, joined Wahyu at the bottom of the square. After several days, enough of the cranium and mandible had been exposed for Rokus to realize that this was no small child; instead, all of its teeth were permanent meaning that this was a fully grown adult. A few weeks later, the team had recovered the rest of this hominin's partial skeleton, the likes of which had never been discovered before. Today, this specimen is referred to as LB1 (Liang Bua 1), and is the holotype specimen for the species Homo floresiensis.

At the time of the discovery, the Liang Bua Research Team included specialists in archeology, geochronology, and faunal identification, but there was no physical anthropologist. Dr. Mike Morwood, the co-leader of the project, invited his colleague at the University of New England in Australia, Dr. Peter Brown, to lead the description and analysis of the skeletal remains. Dr. Brown is an expert on cranial, mandibular, and dental anatomy of early and modern humans and he agreed to apply his expertise to the study of the new bones from Liang Bua. This important scientific work resulted in the first descriptions of these skeletal remains in the journal Nature on October 28, 2004. This work also gave the scientific name, Homo floresiensis, to the hominin species that is represented by the skeletal material from the Late Pleistocene sediments at Liang Bua.

Just before the two Nature articles on Homo floresiensis were published in 2004, the Liang Bua Research Team uncovered additional skeletal material. This included the arm bones of LB1, and several bones of another individual, LB6, including the mandible and other bones of the arm. Drs. Morwood and Brown, and other Indonesian and Australian members of the Liang Bua Research Team, described and analyzed these new skeletal remains of Homo floresiensis and again published their results in Nature on October 13, 2005.

The skeletal evidence suggests that adults of this species had extremely small brains (400 cubic centimeters), stood only about 1 meter (3'6") tall, and weighed around 30 kg (66 lbs). For their height, these individuals have large body masses, and in this regard appear more similar to earlier hominins like "Lucy" (Australopithecus afarensis) than they do to modern humans, including small and large-bodied people. The proportions between the upper arm (humerus) and upper leg (femur) also appear more similar to those in Australopithecus and Homo habilis than those of modern humans.

 

Sebagian besar para ilmuwan berpendapat bahwa manusia hidup sekitar 2 juta tahun yang lalu. Tetapi manusia barangkali berawal dari perkembangan leluhurnya yang hidup pertama kali 4 juta tahun yang lalu. Leluhur pra-manusia adalah mahkluk yang menyerupai manusia yang berjalan tegak dengan ukuran yang kecil.

Para ilmuwan yakin bahwa manusia dan kera besar, seperti simpanse, gorilla, orang utan berasal dari leluhur yang sama. Fosil-fosil makhluk kuno yang menyerupai manusia dan kera besar menunjukkan kesamaan, termasuk kesamaan ukuran otak. 

Kisah evolusi manusia pun dimulai dengan adanya perubahan iklim. Kira-kira 15 juta tahun yang silam suatu jalur hutan tropik mulai mengering ketika jumlah curah hujan menurun. Jalur itu membentang dari pantai timur Afrika menembus Arabia dan India sampai Asia Tenggara. Hutan-hutan yang lebat itu menipis lalu menghilang di seluruh tempat kecuali di daerah paling basah yang berada di tepi-tepi sungai dan danau sehingga terbentanglah daerah luas sabana dan tanah hutan terbuka. Pada awal masa perubahan ekologi ini terjadi evolusi Ramapithecus, yakni mata rantai antara manusia dan primata yang lam-lain.

Para ilmuwan berpendapat bahwa hominid kuno mungkin masih memiliki rambut sebanyak rambut leluhurnya, tetapi badannya lebih kecil dan giginya sangat berbeda. Karena hidup di tanah yang tak berhutan lagi atau pada pinggiran hutan, Ramapithecus terpaksa mengganti makanan khas hutan yang biasanya, yakni dedaunan dan buah-buahan, dengan sayuran dan biji-bijian yang dicarinya di tanah. Mula-mula Ramapithecus hanya melewatkan waktu sebentar setiap harinya untuk makan di tanah; waktu selebihnya dihabiskan dengan berkeliaran, bermain-main, tidur dan mencari tempat berlindung di pepohonan yang sudah dikenalnya. Sikap berdiri tegaknya paling banter tentu masih sempoyongan, walaupun tentunya sikap tersebut lebih mudah dipertahankan pada waktu makhluk itu berlari dengan jarak-jarak dekat, namun, karena Ramapithecus bertampang dan berperi laku mirip kera, banyak ahli antropologi sekarang yakin bahwa makhluk tersebut sudah membawa bibit-bibit Homo sapiens yang akan datang kemudian.

Para ahli antropologi tidak yakin bagaimana terjadinya evolusi dari Ramapithecus ke makhluk yang sangat mungkin merupakan keturunannya, yakni Australopithecus.

Kesenjangan dalam catatan fosil selama beberapa juta tahun memberikan peluang untuk berspekulasi mengenai periode tersebut. Bukti yang ada hanya menunjukkan bahwa Ramapithecus mungkin telah hidup pada masa hanya delapan juta tahun yang lalu, sedangkan bukti bagi Australopithecus diketahui hanya dari masa lima juta tahun yang lalu.

Para ahli biologi evolusi dengan hati-hati berspekulasi bahwa kesenjangan yang lamanya tiga juta tahun itu ditempati oleh suatu leluhur