Group I introns are a distinct RNA group that catalyze their excision from precursor RNA transcripts and ligate the exons. Group I introns have a sporadic and highly biased distribution due to the two intron transfer mechanisms of homing and reverse splicing. These transfer pathways recognize assigned sequences even when introns are transferred beyond the species level. Consequently, introns at homologous gene sites between different host organisms are more related than those at heterologous sites within an organism. We describe the subgroup IE introns of two Chlorella species that are symbiotic green algae (photobionts) of a ciliate, Paramecium bursaria. One strain Chlorella sp. SW1-ZK (Csw.) had two IE introns at S651 and L2449, and the other strain Chlorella sp. OK1-ZK (Cok.) had four IE introns at S943, L1688, L1926, and L2184 (numbering reflects their homologous position in Escherichia coli rRNA gene: S = small subunit rRNA, L = large subunit rRNA). Despite locating on six heterologous sites, the introns formed a monophyletic clade independent of other groups. Phylogenetic and structural analyses of the introns indicated that Csw.L2449 has an archaic state, and the other introns are assumed to be originated from this intron. Some of the introns shared common internal guide sequences, which are necessary for misdirected transfer (i.e., transposition) via reverse splicing. Other introns, however, shared similar sequence fragments further upstream, after the insertions. We propose a hypothetical model to explain how these intron transpositions may have occurred in these photobionts; they transposed by a combination of homing-like event requiring relaxed sequence homology of recognition sequences and reverse splicing. This case study may represent a key to describe how group I intron explores new insertion sites.