Apart from playing a significant role in metabolism, apoptosis, illness, and ageing, Mitochondrial (mt) genomes have emerged as a significant source of data for comparative genomics. With a typical insect mtDNA genome size of less than 16 kb, largely preserved gene completion, and a high rate of nucleotide substitution, this small genome makes it the perfect vehicle for a variety of comparative investigations that have advanced our understanding of genome evolution. Insect mitochondrial genomes are now the most widely utilized molecular markers for population genetics, phylogeography, molecular diagnostics, and phylogenetic investigations because of their relative simplicity in amplification and sequencing during the past two decades. The tRNA molecule has a characteristic folded structure with three hairpin loops like a three-leafed clover. One of these hairpin loops has an anticodon sequence, which can detect and decode an mRNA codon. MITOS webserver is a frequently used software for gene annotation. However, during our analysis of complete mitochondrial genome, the trnH gene was missing from the annotation table generated in MITOS software for several mitogenomes and there fore secondary structures was not made. To circumvent this problem, we searched for alternative software packages and online webservers that can predict the secondary structures of tRNA genes and enable researchers study and analyze gene studies.