Mitochondrial information is more sensitive to short historial periods (as typically it is maternally inherited and therefore the Ne of the population is reduced). However mtDNA actually represent one linked relatively-small segment, and therefore is giving inference about just one locus. Nuclear inference (if based on several genes) is more representative of the organism history, as it is multilocus.

All living entities does not have a mitochondrion but has to have a 16S/18S rDNA.

 sir i am a fisheries student and all the fishes do have both mitochondrion and nucleus, so, in this case why 16s/18s rdna is more prefered than mitochondrial dna???

sir i am asking that which one is the best for phylogenetic study??

It will depend on your question, but there are a bunch of different neutral markers to use. For instance, you can use neutral microsatellites or neutral SNPs...but for a phylogenetic study I will combine it with mitocondrial as well.

Thanks #Maria Cortazar

Mitochondrial information is more sensitive to short historial periods (as typically it is maternally inherited and therefore the Ne of the population is reduced). However mtDNA actually represent one linked relatively-small segment, and therefore is giving inference about just one locus. Nuclear inference (if based on several genes) is more representative of the organism history, as it is multilocus.

Emilio Rolán-Alvarez has given the perfect answer. Additionally though, there are several drawbacks associated with the use of mtDNA in phylogenetic studies which nuclear loci do not suffer from. The following two papers would be a good start to get an overview of these:

Balloux, F., 2010. The worm in the fruit of the mitochondrial DNA tree. Heredity 104, 419-420.

Galtier, N., Nabholz, B., Glemin, S., Hurst, G.D., 2009. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18, 4541-4550.

thanks for the help # serena dool and # Emilio Rolán-Alvarez 

Apart from the very good points raised by Emilio and Serena, another two major point is that mtDNA more likely than not will be constrained by selection. Almost always by purifying selection and sometimes by positive selection, this can of course give a different phylogenetic topology and branch lengths, several reviews on this. e.g. Dowling 2008 and James 2016. Another thing is that mitochondrial-nuclear discordance is much more common that often considered, this can be due to selection, introgression, lineage sorting or sex-biased dispersal. See excellent review by Toews and Breslford