This study was achieved to estimate the phylogenetic relationships of some species of catfish belonging to the order Siluriformes, using small (12S rRNA) and large (16S rRNA) mitochondrial rRNA genes. The length of small mitochondrial rRNA sequences ranged from 832 to 1191 bp. The overall genetic distance was 0.15. The length of large mitochondrial rRNA sequences ranged from 554 to 564 bp. The overall genetic distance was 0.09. Both genes (12S rRNA and 16S rRNA) showed nearly equal A+T composition (53.42 and 53.03, respectively). In addition, both genes displayed A+T composition higher than the C+G. The phylogenetic trees using (12S rRNA) sequences showed that all understudied catfish species and their related GenBank catfish species were grouped according to their genera and families. The same results were found using (16S rRNA) sequences, except for the family Claroteidae which displayed different taxonomic positions. Furthermore, the Monophyly family Claroteidae as well as its position to the other family needs more investigation.