While the mitochondrial genome has been extensively studied since its discovery, the presence of mitochondrial introns in animals wasn’t confirmed until 1982. Further, they were generally thought to be absent from non-bilaterian lineages until 1996. Mitochondrial introns are still poorly studied in non-bilaterian lineages, leading to an incomplete understanding of their actual diversity. After sequencing, we have identified 17 previously undescribed introns within the cox1 gene, across 7 clades of phylum Porifera (sponges). Four of these clades have not previously been known to contain introns. Of the 17 identified introns, 14 are of type I and three of type II. Previous studies had only reported a single instance of a type II intron in Porifera. We propose that these and previously reported introns arose from Horizontal Gene Transfer (HGT) events from ancestral algae species into Porifera. We also report on the first instance of an intron in the cox2 gene of animals. This intron is of type II and is distinct from type II introns found in cox1, which leads us to believe it has arisen from an independent HGT. This study more than doubles the number of species known to contain introns in Porifera and shows that our understanding of intron distribution is still incomplete. Further study of previously under-sampled species is the only way to gain a more complete understanding of this genomic element.