Relations between the Republic and its neighbour Ali Pasha were tense and complicated.
The Ionian Islands, and especially Lefkada, were a common refuge for the sanctuary for klephts and brigands fleeing the Ottoman authorities of the Greek mainland.
With the Islands as a secure base, they often launched raids on the Turkish-held shores.
 In turn, Ali Pasha harassed the Republic's citizens, and imposed heavy tolls on its vessels in the harbours he controlled.

During this period, Ali Pasha in a series of campaigns suppressed the rebellious Souliots, who defied his authority.
Advised by the turncoat Georgios Botsaris, Ali pursued a strategy of encircling the area of Souli with forts and besieging it.
 Already in 1800, the Souliots wrote to Theotokis for aid against the designs of Ali Pasha.
The latter in turn threatened the inhabitants of Parga, to prevent them from lending any aid to the Souliots.
By 1803, the position of the Souliots had grown dire, and they implored the Septinsular Republic for ammunition.
A Souliot embassy visited Mocenigo, conveying an appeal to Tsar Alexander.
Mocenigo gave them some ammunition, but secretly from the Russians; this and later requests for Russian mediation remained unanswered, even as Ali Pasha, with the Sultan's backing, moved to eradicate the last centres of Souliot resistance.
The Souliots who managed to escape from Ali's forces made for Parga, but they were forced to cross the sea to the Septinsular Republic in March 1804, after Ali Pasha threatened to attack the city.
In November 1803, the Republic signed a treaty with Ali Pasha, who was represented by the Metropolitan of Nafpaktos Ignatios.

Approximately 3,000 Souliots settled in the Ionian Islands, mostly in Corfu and Paxoi, where they were provided with farmland.
The warlike Soulioes struggled to fit in their new environment, stealing cattle and firewood from local residents and lamenting the loss of their homeland.
Anxious to expand its influence to the Greek mainland, Russia signed alliances with Himariot and Cham Albanian beys on 27 June 1804.
Souliot refugees were mobilized for an offensive, which was cut short when Ali Pasha learned of the Russian plans and an Ottoman naval squadron made an unexpected appearance off Corfu.

As French–Ottoman relations began to warm in 1805, the Russians began raising native military formations for the defence of the Ionian Islands, enrolling Souliots, Himariots, Acarnanians, and Moreots into the so-called "Greek Legion", which was placed under the command of the Greek-born Major-General Emmanouil Papadopoulos.
In autumn 1805 the Greek Legion participated in the Anglo-Russian invasion of Naples, and in 1806 it fought against the French at the Bay of Kotor.
Relations between the Republic and its neighbour Ali Pasha were tense and complicated. The Ionian Islands, and especially Lefkada, were a common refuge for the sanctuary for klephts and brigands fleeing the Ottoman authorities of the Greek mainland. With the Islands as a secure base, they often launched raids on the Turkish-held shores.  In turn, Ali Pasha harassed the Republic's citizens, and imposed heavy tolls on its vessels in the harbours he controlled.
During this period, Ali Pasha in a series of campaigns suppressed the rebellious Souliots, who defied his authority. Advised by the turncoat Georgios Botsaris, Ali pursued a strategy of encircling the area of Souli with forts and besieging it.  Already in 1800, the Souliots wrote to Theotokis for aid against the designs of Ali Pasha. The latter in turn threatened the inhabitants of Parga, to prevent them from lending any aid to the Souliots. By 1803, the position of the Souliots had grown dire, and they implored the Septinsular Republic for ammunition. A Souliot embassy visited Mocenigo, conveying an appeal to Tsar Alexander. Mocenigo gave them some ammunition, but secretly from the Russians; this and later requests for Russian mediation remained unanswered, even as Ali Pasha, with the Sultan's backing, moved to eradicate the last centres of Souliot resistance. The Souliots who managed to escape from Ali's forces made for Parga, but they were forced to cross the sea to the Septinsular Republic in March 1804, after Ali Pasha threatened to attack the city. In November 1803, the Republic signed a treaty with Ali Pasha, who was represented by the Metropolitan of Nafpaktos Ignatios.
Approximately 3,000 Souliots settled in the Ionian Islands, mostly in Corfu and Paxoi, where they were provided with farmland. The warlike Soulioes struggled to fit in their new environment, stealing cattle and firewood from local residents and lamenting the loss of their homeland. Anxious to expand its influence to the Greek mainland, Russia signed alliances with Himariot and Cham Albanian beys on 27 June 1804. Souliot refugees were mobilized for an offensive, which was cut short when Ali Pasha learned of the Russian plans and an Ottoman naval squadron made an unexpected appearance off Corfu.
As French–Ottoman relations began to warm in 1805, the Russians began raising native military formations for the defence of the Ionian Islands, enrolling Souliots, Himariots, Acarnanians, and Moreots into the so-called "Greek Legion", which was placed under the command of the Greek-born Major-General Emmanouil Papadopoulos. In autumn 1805 the Greek Legion participated in the Anglo-Russian invasion of Naples, and in 1806 it fought against the French at the Bay of Kotor.
Septinsular Republic