The Ark of the Covenant initially housed two tablets that had written upon them, with the finger of God, the Ten Commandments (Exodus 25:16). These tablets, written on both sides (Exodus 32:15), were actually a second copy made by the Eternal after Moses broke the original ones due to Israel's sins (verse 19).
God, in order to quell complaints by the Israelites against Moses, commanded each of the twelve tribes give him a staff with the tribal leader's name written upon it (Numbers 17). The staff for the tribe of Levi, however, was to have Aaron's name written upon it. The Lord's plan was to show, through Levi's staff, that Aaron and his tribe were specially chosen, amongst all Israel, to serve Him.
Miraculously, a day after the staffs were placed in front of the Ark of the Covenant, Aaron's staff not only sprouted but also budded, blossomed, and produced almonds!
And it came to pass on the next day Moses went into the tabernacle of witness. And behold, the rod of Aaron for the house of Levi had budded and had brought forth buds, and had bloomed blossoms, and had yielded almonds (Numbers 17:8, HBFV throughout).
According to the Apostle Paul, Aaron's rod was ultimately placed inside the Ark of the Testimony (Hebrews 9:4). A golden pot which contained manna, the "bread of heaven" God rained on the Israelites to feed them in the wilderness, seems also to have been placed into this holy ark (Exodus 16:32, Hebrews 9:4).
Mystery of missing contents
The Bible makes a rather startling statement regarding the contents of the ark when it was moved into the temple's Holy of Holies. This move took place c. 959 - 958 when King Solomon held an immense dedication ceremony for the newly built place to worship God.
There was nothing in the ark except the two tablets of stone which Moses put there at Horeb (Mount Sinai), when the Lord made a covenant with the children of Israel when they came out of the land of Egypt (1Kings 8:9).
What happened to Aaron's budded rod and the jar of manna the New Testament declares was in the Ark of the Covenant? Why weren't they mentioned in 1Kings8?
But behind the second veil was a tabernacle which is called the holy of holies, containing a golden censer, and the ark of the covenant, which was overlaid on all sides with gold; in which was the golden jar containing the manna, and the rod of Aaron that had sprouted, and the tablets of the covenant (Hebrews 9:3 - 4, HBFV).
The lack of a definitive Biblical answer solving this ark mystery has led to Bible commentaries offering their own theories regarding the absence of the rod and manna in 1Kings 8.
Some commentaries believe that Aaron's rod and a jar of manna were never placed inside the Ark of the Covenant but were located near it. They are not mentioned in 1Kings 8 because they were simply moved into the Holy of Holies, along with the ark, at the dedication ceremony of Jerusalem's temple.
Some commentaries attempt to reconcile a straightforward meaning of Hebrews 9:4 with the Old Testament record. They speculate that at one time the rod and manna were inside the Holy Ark but were removed sometime before the dedication ceremony. A variation of this theory states these objects had been outside the ark since its creation but were placed inside it sometime after the temple was dedicated.
The Bible Knowledge Commentary offers yet another twist in an attempt to explain the absence of the rod and manna in 1Kings 8:9. One of Israel's enemies, like the Philistines (see 1Samuel 4 - 6), could have removed these items from the Ark of the Covenant and never gave them back to God's people.
A rather strange tradition
The 1906 Jewish Encyclopedia, in its article on the Ark of the Covenant, relates a rather odd Islamic tradition regarding what was inside this holy container.
"Others said that there was in the Ark a figure of chrysolite or ruby with the head and tail of a shecat and with two wings. It would utter a moaning sound, and the Ark would rush toward the enemy with the Israelites following it. When it stayed, they stood and were at ease, and victory came."