Despite their importance in a wide range of living organisms, self-cleaving ribozymes in human genome are few and poorly studied. Here, we performed deep mutational scanning and covariance analysis of two previously proposed self-cleaving ribozymes (LINE-1 and OR4K15). We found that the functional regions for both ribozymes are made of two short segments, connected by a non-functional loop with a total of 46 and 47 contiguous nucleotides only. The discovery makes them the shortest known self-cleaving ribozymes. Moreover, the above functional regions are circular permutated with two nearly identical catalytic internal loops, supported by two stems of different lengths. This new self-cleaving ribozyme class, named as lantern ribozyme for their shape, is similar to the catalytic region of the twister sister ribozymes in term of sequence and secondary structure. However, the nucleotides at the cleavage sites have shown that mutational effects on lantern ribozymes are different from twister sister ribozymes. The discovery of lantern ribozymes reveals a new ribozyme class with the simplest and, perhaps, the most primitive structure needed for self-cleavage.