Alytus surroundings were settled by first inhabitants in the first centuries after Christ. This is evidenced by the Bakšiai settlement dated back to the III th –IV th centuries, Radžiūnai Mound with settlement dated back to the III th –V th centuries and Alytus Mound with settlement, dated back to the VII th–XI th centuries.
The first historical record of Alytus dates back to 1377 m. when it was mentioned in the Chronicles of Wigand of Marburg.
The wooden castle that stood on Alytus Mound was first mentioned in 1384. With the castles of Merkinė, Nemunaitis, Punia, Birštonas, Darsūniškis and Kaunas it formed a system of the most important roads to Trakai and Vilnius for defense against the Crusarder attacs. In the Jogaila Privillege to Skirgaila, which was granted in 1387, Alytus is called a town, also the land of Alytus was mentioned along with the Grand Duke’s castle in the center.
After the Battle of Grunwald (1410), iwhen the threat of the Teutonic Order disappeared, the Alytus Mound lost its defensive significance. The town located at the castle gradually grew. After expansion to Užnemunė, the town started to develop on the left bank. The development of the town at that time was also influenced by two Alytus manors, which stood on the right and left bank of the Nemunas River.
In the XVI a. century Alytus belonged to various ownes: the Marshal of the Region Jonas Zabžezinskis, Queen Bona, Žygimantas Augustas (Sigismund Augustus) and Barbora Radvilaitė. Based on the inventories of the town of the second half of the XVI century according to the silver tax paid Alytus can be described as a small town with a population of over 1000 inhabitants. Most of them were engaged in crafts and trade. In 1524 the first Catholic church in Alytus was mentioned and in 1595 the first school was established.
On 15 June 1581 Grand Duke of Lithuania and King of Poland Stefan Batory granted the town the city rights based on the Magdeburg Law.
This marks the beginning of a new phase of development. The city received the self-government right and the coat of arms - a white rose on a red background. The townspeople were told to build a town hall, in which the magistrate, a self-governing body, was to meet. In 1589 the economy of the royal table of Alytus was established, which facilitated the economic development of the city.
In XVII–XVIII centuries the city often suffered from various disasters: war, plague, fires. All of this influenced the development of the city, the population and the territory decreased. In 1775 district courts were moved to Alytus from Trakai and Merkinė. In 1776 the Seimas of the Commonwealth of the Two Nations adopted the Constitution, according to which many cities, including Alytus, were deprived of the autonomy rights. On the basis of the resolutions of the Four-year Seimas (1788-1792), the Constitution of May 3, 1791, in 1791–1792 citizens of Alytus city tried to restore the autonomy rigths. The King of Poland and the Grand Duke of Lithuania Stanisław August Poniatowski did not grant Alytus the privilege of renovation therefore the city self-government was not legalized. In the third partition of Poland and Lithuania, in 1795, the town was divided between the Russian Empire and the Kingdom of Prussia.
More than a hundred years after the division of the Republic of Two Nations, the two parts of the city - the first and the second Alytus - developed differently
In 1796 most of cities in Lithuania were classified as towns (“miestiechko”) and handed over to the manor administration. The town of Alytus (the First Alytus) was assigned to the Lelioniai Key of Trakai County. In 1861 after the abolition of corvee labour the parishes were established throughout the Russian Empire and the First Alytus were assigned to the Aleksandrovsk (now Alove, Alytus region) parish. In 1870, Russia adopted the Law on Cities, which came into force in Lithuania in 1876. The scare historical sources preserved reveal that the population of this part of the city elected the elder and the city council at the end of the XIX th century, and at the beginning of the XX th century they elected the village elder. The left part of the city (the Second Alytus) came to the Kingdom of Prussia and later to the Duchy of Warsaw founded by Napoleon. The Autonomous Kingdom of Poland was established instead of the Duchy of Warsaw. By a resolution of the Congress of Vienna in 1815. it was incorporated into the Russian Empire with autonomous rights. The town was attributed to the province of Augustów, later to the province of Augustów, and since 1867 to Suwalki Province, Kalvarija County. With the establishment of the gminas (parishes) in the Kingdom of Poland, Alytus became the center of gmina. The inhabitants of this part of the city insisted on regaining their self-government and the coat of arms of the city. There was a magistrate until 1870. For several centuries the Second Alytus was considered a suburb of the First Alytus. According to the data of the population census conducted in the Russian Empire the First Alytus has a population of 1 435, and the Second Alytus has a population of 2 010 citizens.
Thanks to its strategic position at the end of the XIX th century Alytus was transformed into a third class border fortress by the order of the tsarist government. On each side of the Nemunas River there were 3 barracks, on the left bank of the Nemunas River there were 4 forts and 2 batteries. Highways, railway, 3 bridges over the Nemunas River were built. All these constructions also benefited the city: the population increased, trade and residential construction expanded. The first small industrial enterprises have been established.
During the World War I, Alytus was occupied by German troops. The German military administration re-united Alytus into a single administrative unit, relocating the county center from Kalvarija. The Germans built a power plant in the city.
The emerging Lithuanian state had to defend its freedom with a weapon. Alytus also played an important role in these battles. Since December 1918 the Ist Land force unit started to have been formed in Alytus. Along with the German volunteers on February 12-15, 1919 they stopped the attack of the Red Army units near Alytus. In 1919-1920 Alytus again played a major role in the fighting against Poland. At that time the units of Lithuanian Armed Forces were based in Alytus barracks.
In the interwar period, Alytus became the center of Dzūkija.
In 1931 it became a recognized first-line city and in 1932 it was declared a resort. The town had a gymnasium, several elementary schools, a higher forestry school, a lower agricultural school. Trade has also expanded. Forest and agricultural processing companies dominated in the industry. The city authorities paid great attention to the order in the city: the streets were under construction, the city park was established, and construction were underway. Various cultural, religious and national organizations were active in the city's cultural and social life. The units of the Lithuanian Armed Forces based in Alytus also played an important role in the life of the city. The Second Unit of the Duchess Birutė became a unique symbol of the city.
Political unrest at the beginning of World War II was also related to Alytus. At the end of 1939 the largest USSR military unit was located in the city. During the first Soviet occupation (1940-1941), a large number of the town's inhabitants were arrested and deported, industrial and commercial enterprises were nationalized.
In 1941 when Germany attacked the Soviet Union Alytus was severely ruined. During the German occupation many people were killed, taken to Germany for work. At the end of the war, some emigrated to the West.
The second Soviet occupation began in July 1944. The population of Alytus again suffered from repressions and deportations. Some people became involved in resistance battles. By the decision of the Soviet Lithuanian authorities Alytus became an industrial center. Large industrial companies have been established over several decades. The city was growing rapidly: the population was growing and new urban districts were being built. In 1977 Alytus became a Republican Administered City.
After Lithuania regained its statehood in 1990 Alytus City Municipal Council had to solve new problems. With the beginning of economic reforms most companies were privatized. Many major industrial companies went bankrupt during the economic crisis. Today the city is dominated by light industry, wood processing, and food industry companies. Much attention is paid to the image of the city: streets, parks, care about education, school renovation. A high non-university school Alytus College was established in the city. Youth, social, cultural, national organizations are active. Today Alytus is the political, economic, cultural and educational center of Southern Lithuania.