Abstract: Phylogenetics studies the evolutionary relationships between species. The nucleotide substitution models in phylogenetics usually assume that evolutions of sequences have neither missing nor censored, which is hard to be satisfied in fact. Facing to the fact above, we use an EM algorithm to estimate parameters, to construct a fine phylogenetic tree of the sequences which have the same length after deletions and insertions. Main points of this paper is to estimate best parameters of DNA sequences having censored data for Jukes-Cantor Model and Kimura Model under the conditions of rooted tree and unrooted tree respectively.