The history of the current Zypliai Manor begins from the Old Zypliai Manor, which, since 1806, was the property of the Grand Duke of Lithuania Juozapas Poniatovskis who received it for his war merits with Napoleon’s army. In 1813, after Juozapas Poniatovskis death, the estate was given to his sister Marija Teresa Tiškevičienė, who lived in Paris and rarely visited Zypliai. Soon she sold Zypliai to Polotsk province landowner Jonas Bartkovskis. The latter established a Manor in Palankiai village, near Lukšiai, and named it the New Zypliai. In 1855, Jonas Bartkovskis suddenly died and was buried in Lukšiai cemetery. After the unexpected death of Jonas Bartkovskis, in 1855, Zypliai Manor became the property of his step-daughter Joana Wolfer – Kučinskienė. Later, Zypliai Manor became the property of her daughter Liudvika Ostrovskaja. She sold the manor to count Tomas Potockis who reconstructed it between XIX – XX century, making it more magnificent and giving the manor original Neo – Baroque forms. Count Tomas Potockis was an educated and progressive landlord who studied political economy in the University of Tartu and later furthered his knowledge on agriculture in the University of Halle. Since 1900, he was one of the organizers and managers of Suvalkai land association, he published brochures with farming tips in Polish and Lithuanian languages, and was the establisher of the first vegetable canning factory in the lands of the former Lithuania – Poland state near Warsaw, which operated until war. He communicated with painters and liked to paint himself, as well as write drama works in his free time. One of his scripts was even during the production of a play in Warsaw, whose premiere he never got to attend due to his sudden death. After the death of Tomas Potockis, the manor was managed by his wife Pelagija Bžožovska-Potocka until the First World War.
After the First World War, Zypliai Manor was used by various organizations. In 1919, a priest seminary was transferred from Seinai to Zypliai which operated here until 1922. From 1924 to 1944, Zypliai manor was used as a lower agricultural school, whose director and administrator of Zypliai Manor was Justinas Saliamonas Banaitis, the son of Independence Act signatory Saliamonas Banaitis.
In 1981, sculptor Vidas Cikana moved to Lukšiai and started taking care of the manor buildings that previously belonged to the collective farm. In 1990, after Lithuania regained its independence, its self-government was also restored, and Vidas Cikana was elected to be the town‘s governor who put a lot of effort to transfer all the Zypliai Manor buildings from Lukšiai agricultural company to Lukšiai eldership on 1 March 1993. Due to the efforts of Lukšiai town governor and folk artist Vidas Cikana, the manor was gradually revived. Manor and park restoration works began in 2002. On 26 March 2003, Folk art exhibition was organized in the stables of Zypliai Manor, which was attended by guests from across Lithuania. 1090 folk art works were exhibited in the show which was organized for the very first time in this location. Lukšiai cultural centre began its cultural activities since the opening of the gallery in Zypliai Manor.
Soon after, on the initiative of head of Lukšiai eldership Vidas Cikana, discussions began to take place regarding the restoration of buildings and their adaptation to the needs of the society. In 2004, a project was already underway for the reconstruction of Zypliai Manor, however the funds for its implementation were continuosly delayed. After many years of discussions and negotiations, an investment project was prepared in 2009. Whereas in 2010, agreement for the funding and administration of the project „Zypliai Manor adaptation for cultural tourism“ was signed.
Zypliai Manor was restored during this project – exterior of both chambers and former kitchen building were renovated, and the stable roof was replaced. On this occasion, a conference, concerts of various genres, folk art fair and exhibitions were organized.