Even at the time Old Panama was founded in 1519, the small port at the mouth of the Rio Abajo was filling with silt. Sailing ships of greater draught used the anchorage at Perico Island.

In 1586, Philip II, King of Spain, sent a decree ordering that no ship of more than 3000 arrobas (about 38 tons) should enter the port of Old Panama.

The Isles of Perico, as they were known until this century, appear on many early maps. Often first a dot marked "Perico" (or "Perica") is shown. A Dutch map of 1620 shows "Paerto Perico". Sometimes Naos also appears, occasionally as "Isnao".

There are four islands in this group, although they are often thought of as being three. Culebra. the smallest, lies south of Naos. Where it formerly was joined to Naos by a sandbar, it now has a causeway and seems a part of the larger island. "Culebra" means "snake". Malaspina, in 1790 call it "Culebrillo", little snake.

Naos, the first island reached by the causeway from Fort Amador, was known in the early days, for the beach on it’s east side. It was connected to Perico at low water by a sandbar. Ships were beached here for repairs and careening thus the name "Naos" or "Ships".

Perico, next on the main causeway from Naos, probably was named for the flocks of parkeets that screeched in its trees. However, it might also have been named after ta type of curl once worn by women.

Flamenco or sometimes referred to as "Isla de Flamencos", perhaps was a favorit with Flamingos In the early days of the port.

The anchorage commonly used was northeast of Perico in a line with the point of the Bovedas in (new) Panama City. There were from five to seven fathoms of water and a good bottom. The islands sheltered the anchorage from the prevailing wind.

Some details about the islands and the port are found in the "Report on Panamanian Coast" by Captain Diego Ruiz d Campos in 1631.

"Northeast-southwest with the city of Old Panama and two leagues from it and north-south with the Rio Grande (now the mouth of the Canal) a league is at the port of Perico where anchor the ships that come with cargo for Panama - those of His majesty as well as those of private owners - and treasure and the other things that are brought for unloading in medium boats."

"As soon as the merchant ships arrive at the port of Perico, the y are unrigged of all sails shrouds and other rigging that they have until they are down to the bar mast, and all is stored away sow that they will not rot with the many heavy rains. Because in this port of Perico is where the ships receive the most damage and deterioration in the South Sea, as much from the many shipworms that greatly damage the hulls as from the heavy rains.."

In describing the islands, he states that they are "full of groves of trees of such little importance that there is not in all of them one tree that is of use for repairing a ship or boat. All of these islands have water though so little that the crew of the merchant ship having only 16 persons cannot be sustained by it and so they go with small vessels and boats to bring it from other parts of the coast and from the island of Taboga."

"Perico is populated with some houses or warehouses that the owner rents to the ships for storing and protection their provisions while they are careening".

"The other island that is behind Perico and an arquebus shot to the southeast from it is called the Island of Flamingos, which also is inhabited because the owner has his house and a large plantation of plantain trees here from which he draws a profit from what he sells to the people of the ships and boats that arrive here, and also from what he brings to the city to sell".

"The third is called the Island of Ships, and is called by this name because it has a beach of white sand on the eastern part where since early times it has been the custom to beach the ships on stanchions and repair and careen them and only this island has the beach referred to because the other two, do not have beaches but each one a cove full of small stores where people disembark and embark."

In 1637 on of the few Englishmen bale to travel freely in Spanish America at this time, the Dominican priest Thomas Gage, took passage from the Gulf of Salinas on a Panama frigate returning to Panama with a cargo of pita and food.

"In he evening we got to Puerto de Perico where we cast anchor, expecting to be searched in the morning, but that night (the master of the ship having gone to shore) the wind turned back and blew so strong that we lost our anchor and were driven back almost to La Pacheque. We came once more to Perico, and after being searched, we went on with full sail to Panama."

Being near the port and without an anchor in our ship, the wind once more blew us back, and had not the ship master sent us an anchor we had gone again to Pacheque or further. But with the anchor, we stayed all that night at Perico. Thither is brought the chief treasure of Peru in tow or three great ships, which lie at anchor at Puerto de Perico".

In 1671, Old Panama was destroyed and it was decide to build the new city at a better location. The proximity to the anchorage at Perico was one of the factors considered in the selection of the present site. Lionel Wafer, who visited these waters as a buccaneer surgeon, thought it worth a comment in his book.

"The chief advantage which New Panama hath above the old is an excellent road for small ships as good as a harbor, for which it is beholden to the shelter or the neighboring isles of Perica which lie before it three in number in a row parallel to the shore, there is a very good distance from the town, but between the road and the town is a shoal or spit of land so that ships cannot come near the town but be nearest to Perica, but by this means the town has them less under command".

In 1680 a party of about 330 buccaneers crossed the isthmus on foot. Using Indian cayucos and a captured Spanish ship some of the party went to the Pearl Islands and the rest toward Panama City. There were five large ships and three barks at Perico. Several of the large ships, were unmanned and one of the barks ran away. After a fight of about five hours, the Spanish ships surrendered. The buccaneers lost 20 men, including Peter Harris, one of their captains. They landed on Perico to bury Harris and the other dead. One of the Spanish ships, the Santisima Trinidad, was converted into a hospital, and the buccaneers rested at Perico about ten days waiting for the rest of the party to arrive from the Pearl Islands. Lionel Wafer and William Dampier who were members of this expedition later wrote accounts of their adventures.

Apparently the Spanish lacked the power to protect the bay or even the port and had to remain behind the wall of their new city in frustration. However, Dampier gives an account of a Spanish attempt to accomplish by trickery what they were unable to do by strength.