Undoubtedly there was at first some inscription to mark the tomb, but in the course of the years any slabs with inscriptions were permitted to disappear entirely from the graves of Columbus, his son and grandson, and the very existence of their remains in the cathedral became a matter of tradition. It is possible that the epitaphs disappeared at some time when the pavement of the church was renewed, or when damages inflicted by earthquake shocks were repaired, or when changes were made in the windows and doors about the main altar, or when the higher altar platform was extended to reach the desks on which lie the Gospels and Epistles. At any such times the slabs over the burial vaults may have been broken or laid aside and never replaced. It is also possible that they were intentionally removed in order to guard against profanation of the tombs by enemies in time of war or by West Indian pirates, who captured and sacked stronger cities than Santo Domingo. In 1655 when an English fleet under Admiral William Penn appeared before the city and landed an army under General Venables, there was great excitement and fear in Santo Domingo, and the archbishop ordered that the sacred ornaments and vessels be hidden and that "the sepulchres be covered in order that no irreverence or profanation be committed against them by the heretics, and especially do I so request with reference to the sepulchre of the old Admiral which is on the gospel side of my holy church and sanctuary," That other tombs were hidden, whether at this time or another, was shown in 1879, when, on repairing the flooring in the chapel of the "stone bishop" in the cathedral, the slab indicating the grave of the Adelantado Rodrigo de Bastidas, the explorer, was found concealed under a stone, and it was discovered that the epitaph of Bastidas on a board which from time immemorial had hung on the wall of the chapel was an incorrect copy of the original graven on the burial slab. From the words of the archbishop it appears possible that the sepulchre of Columbus was marked in some way in 1655, although even then there may have been nothing, since the prelate saw fit to specify the point in the church where the tomb was situated.
The first document in which tradition appears invoked for designating the burial place is the record of a synod held in 1683, which contains the following clause: "this Island having been discovered by Christopher Columbus, illustrious and very celebrated throughout the world, whose bones repose in a leaden box in the sanctuary next to the pedestal of the main altar of this our cathedral, with those of his brother Louis Columbus which are on the other side, according to the tradition of the old people of this Island." The synod and tradition were not strong in Columbus genealogy when they referred to Louis Columbus as the brother instead of the grandson of the Discoverer, and it is noticeable that no mention is made of the son Diego Columbus. It may be remarked, in passing, that the body of Bartholomew Columbus, brother of the Admiral, was deposited in the convent of San Francisco in Santo Domingo, upon his death in 1514, and while some writers suggest it may have been taken to Spain, there is nothing to indicate that it was ever given sepulture in the cathedral of Santo Domingo.
After the lapse of another century tradition referred to two sepulchres, one of Christopher Columbus, on the right side of the altar, the other of his brother or son, on the left side of the altar. Moreau de Saint-Méry, a French diplomat and statesman, who lived in the French colony of St. Domingue for some years during the decade of 1780 to 1790, in his book "Description de la partie espagnole de l'isle Saint-Domingue" states that, being desirous of obtaining accurate information with reference to the tomb of Columbus, he addressed himself to José Solano, an ex-governor of the colony, then in command of a fleet in the insular waters; that this official wrote a letter to his successor in the governorship, Isidoro Peralta, and that he received the following answer:
"SANTO DOMINGO, March 29, 1783.
"My very dear friend and patron:
"I have received the kind letter of Your Excellency of the 13th of this month, and did not answer immediately in order to have time to ascertain the details it requests relative to Christopher Columbus, and also in order to enjoy the satisfaction of serving Your Excellency as far as is in my power and to permit Your Excellency to have the satisfaction of obliging the friend who has asked for those details.
"With respect to Christopher Columbus, although the insects destroy the papers in this country and have converted whole archives into lace-work, I hope nevertheless to remit to Your Excellency the proof that the bones of Columbus are in a leaden box, enclosed in a stone box which is buried in the sanctuary on the side of the gospels and that those of Bartholomew Columbus, his brother, repose on the side of the epistles in the same manner and under the same precautions. Those of Christopher Columbus were transported from Seville, where they had been deposited in the pantheon of the dukes of Alcala after having been taken there from Valladolid, and where they remained until their transport here.
"About two months ago, in working in the church, a piece of thick wall was thrown down and immediately reconstructed. This fortuitous event was the occasion of finding the box of which I have spoken, and which, although without inscriptions, was known, according to a constant and invariable tradition, to contain the remains of Columbus. In addition I am having a search made to see whether in the church archives or those of the government some document can be found which will furnish details on this point; and the canons have seen and stated that the greater part of the bones were reduced to dust and that bones of the forearm had been distinguished.
"I send Your Excellency also a list of all the archbishops which this island has had and which is more interesting than that of its presidents, for I am assured that the first is complete, while in the second there are voids produced by the insects of which I have spoken and which attack some papers in preference to others.
"I also refer to the buildings, the temples, the beauty of the ruins and the motive which determined the transfer of this city to the west bank of the river which constitutes its port. But with reference to the plan requested by the note there is a real difficulty, as this is forbidden me as governor; the superior understanding of Your Excellency will comprehend the reasons, etc."