An encrypted database system constituted with a client terminal and an encrypted database server mutually connected to each other, wherein the client terminal comprises: recording means for recording an encryption key in advance; column encryption means for encrypting data on an a-th column of a first table and data on a b-th column of a second table inputted from outside by using the encryption key, and outputting the encrypted tables to the outside; and encrypted table natural joining request means for generating a table joining key containing a column public key and a column private key generated by the encryption key from table identifiers of the first and the second tables and column identifiers of the a-th and b-th columns, and outputting, to the encrypted database server, a natural joining request text for requesting natural joining of the a-th column and the b-th column of the encrypted first table and second tables by including the table joining key, wherein natural joining means to perform equi-joining of the first and second tables under the condition that an element of the a-th column and an element of the b-th column are equivalent, and wherein duplicating columns are omitted when performing the equi-joining, and the encrypted database server comprises: data reception means for receiving the encrypted first and second tables from the client terminal and recording the encrypted tables; and encrypted table natural joining means for executing the natural joining of the encrypted first and second tables according to the natural joining request text by employing the table joining key, wherein the system involves bilinear mapping and scalar multiplication when judging if the element of the ath and bth column are equivalent and wherein the groups are cyclic groups of order p, where p is a prime number. recording means for recording an encryption key in advance; column encryption means for encrypting data on an a-th column of a first table and data on a b-th column of a second table inputted from outside by using the encryption key, and outputting the encrypted tables to the outside; and encrypted table natural joining request means for generating a table joining key containing a column public key and a column private key generated by the encryption key from table identifiers of the first and the second tables and column identifiers of the a-th and b-th columns, and outputting, to the encrypted database server, a natural joining request text for requesting natural joining of the a-th column and the b-th column of the encrypted first table and second tables by including the table joining key, wherein natural joining means to perform equi-joining of the first and second tables under the condition that an element of the a-th column and an element of the b-th column are equivalent, and wherein duplicating columns are omitted when performing the equi-joining, and the encrypted database server comprises: data reception means for receiving the encrypted first and second tables from the client terminal and recording the encrypted tables; and encrypted table natural joining means for executing the natural joining of the encrypted first and second tables according to the natural joining request text by employing the table joining key, wherein the system involves bilinear mapping and scalar multiplication when judging if the element of the ath and bth column are equivalent and wherein the groups are cyclic groups of order p, where p is a prime number. data reception means for receiving the encrypted first and second tables from the client terminal and recording the encrypted tables; and encrypted table natural joining means for executing the natural joining of the encrypted first and second tables according to the natural joining request text by employing the table joining key, wherein the system involves bilinear mapping and scalar multiplication when judging if the element of the ath and bth column are equivalent and wherein the groups are cyclic groups of order p, where p is a prime number.