The history of the Town is shrouded in mysteries due to lack of written evidences or documentation. Popular stories say that a group of early settlers led by warrior Ajay Pal (also called Ajepal), brother of King of Ajmer, Rajasthan arrived and settled there around ad 650 or 805 (Samvat 862). Slowly the settlement flourished and became a center of trade and commerce. Due to its prosperity and wealth it was often target of invasion of Khalifa clan warriors. As the founder of the settlement, and later the ruler of the town, Ajay Pal dedicated his life to protect the town. It's believed that he established the first coastal security center in Kutch somewhere near Anjar. Ajay Pal died due to a mortal wound suffered while fighting Khalifas in Vikram Samvat 741 (around ad 685). Due to his efforts in protecting the town and surrounding area from invaders, and his selfless sacrifice, he is worshiped as a saint and his tomb (also called Samadhi in Hinduism) and temple is located on the outskirts of the town. He is fondly known as the ruler of the town till date.

In the course of history, Chauhan clan lost the power in Anjar. At different points of time in history, the town was ruled by various clans such as Solanki, Vaghela, Chawda, before finally it went to the more powerful warrior clan Jadeja who gained control of whole Kutch region. The town was declared capital of the Kingdom of Kutch in 1545 by KingKhengarji I. The town was fortified by Desalji early in the eighteenth century. The fort wall was sixteen feet high and six feet thick. In 1800 the town, port, and dependencies of Anjar were granted to Fateh Muhammad, who busied himself in extending its trade and establishing the harbour of Tuna. The town served as the Capital of the Kutch region on and off, until finally a nearby settlement namely Bhuj permanently became the capital city of the region. Anjar then served as second largest settlement in the region, and was pushed to the third rank after the rise of the Kandla Port and nearby Gandhidham city which serves as the powerhouse for the regional economy at present.

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