In this study, we delve into the characterisation of mitochondrial related organelle (MRO) in Ascetosporea (Rhizaria) by inferring the energy metabolism of Paramikrocytos canceri, a close relative of Mikrocytos mackini. P. canceri infects the antennal gland of the edible crab juveniles (Cancer pagurus) creating huge swelling leading to the death of the individual. Genomic and transcriptomic Illumina sequence data were generated from healthy (claw muscle) and infected tissues (antennal gland) of C. pagurus juveniles.Using an in-house bioinformatic workflow we were able to generate highly complete P. canceri genomic data and perform the first parallel genomic and transcriptomic study for these economically important marine parasites. The data enabled us to reconstruct the energy metabolism of P. canceri and find additional genes and pathways conserved in M. mackini (e.g., lipid biosynthesis, a complete glycolytic pathway). Based on the identified gene repertoire and phylogenetic analyses, we could infer that the MRO of P.canceri and M.mackini are very similar, and probably originated in their common ancestor. Considering its drastic metabolic reduction this MRO highly resembles a mitosome but with several novel features such as for example the ability to synthesize fatty acids. Yet, the most notable discovery was that two of the energy producing steps of glycolysis are deviated into the MRO. Mitochondrial targeted glycolytic enzymes were identified in protists with hydrogen producing mitochondria or the aerobic mitochondria of ciliates (Apicomplexa) but are for the first time described in such extremely reduced MRO.