Upon the breaking out of the rebellion in 1641 Sir Edward Denny collected his English tenants and the loyal Irish, and they fortified themselves in the two castles. Lady Denny and her children went to England, while Sir Edward joined the President. His step-father, Sir Thomas Harris, took command of the Tralee garrisons, but it was not until early in the following year that the Irish laid siege to the town, under the command of Florence Carty with six hundred men. The guns of Short Castle opened fire, but nevertheless the Irish raided the town. They stripped or murdered all the inhabitants they captured, and hundreds fled to the two strongholds for protection. Upon the 10th of February a spy named Laurence gained admittance to the larger castle, on the plea of seeing the Governor, who was asleep. He carried a pass from the rebel poet, Pierce Ferriter, who commanded the Irish forces in the district. His movements at length awakening suspicion he was taken prisoner. Shortly after this the Irish took possession of the town during the night. The guns of both castles played with little effect, and some of the inhabitants were drawn up into Short Castle by ropes. The Provost, who had left the town to see to some outlying property, was prevented returning, and Sir Thomas Harris had command of both castles, a line from the top of each conveying letters from one fortress to the other. About four hundred persons fled to the strongholds, so that the provisions intended to last two years gave out in seven months. Water failed, and although thirteen wells were sunk twenty feet each, only thick black water could be procured. Captain Ferriter and a townsman of Tralee demanded a parley with Sir Thomas and asked him to surrender, but he refused. They then hauled “sow” engines against the strongholds. The one sent against the great castle was smashed by a small cannon ball, and a cooper in Short Castle dislodged a pinnacle of the building on the top of the other, which they afterwards burnt. The Irish lost about twenty men and their engines in the attack. An effort was made to relieve the town by sea, but the small force sent for the purpose was entirely routed. When the siege had lasted about six months Sir Thomas Harris fell ill and died through bad water and anxiety. Immediately after the provisions giving out the garrisons capitulated, the terms being their lives and a suit of clothes each. Most of them joined Colonel Crosbie in Ballingarry fortress on an island in the Shannon. Of the six hundred within the castles of Tralee three hundred died during the siege. They were reduced to eating bran, tallow, and raw hides. The castles were burnt upon being surrendered.