On 4 April 1990, an Isleña Airlines de Havilland Canada DHC-6 Twin Otter (registered HR-ALH) landed in the water short off the runway at Útila Airport, following a scheduled passenger flight from La Ceiba with 18 passengers on board. The two pilots claimed to have been blinded by the sun, thus misjudging the remaining distance to the runway. All occupants of the aircraft could be saved.
On 3 March 1997, an Isleña Airlines Let L410 Turbolet (registered HR-IAS) did not gain sufficient height upon take-off from Golosón International Airport for a scheduled passenger flight to Puerto Lempira with 19 passengers on board. Following the retraction of the landing gear, the two pilots had applied a wrong engine power setup, and were forced to bring the aircraft down again in a belly landing, during which it was damaged beyond repair.