The present invention provides a category of cyanine dyes having the following general structural Formula I, wherein X is defined as C(CH3)2, O, S or Se; m is an integer from 1 to 18, R1 and R2 are each independently chosen from H, C1-18alkyl, OR7, C1-6alkyl-OR7 or halogen; R3 is pyrrolyl, imidazolyl, piperidinyl, piperazinyl, morpholinyl, guanidino, NHR5 or N(R6)2; R4 is C1-18alkyl, benzyl or (CH2)mR3; R5 is saturated and/or unsaturated, straight-chained and/or branched-chained C1-18alkyl, hydroxy alkyl, mercapto-alkyl, amino alkyl, acyl, phenyl, naphthyl or benzyl; R6 is a C2-18alkyl; R7 is H or a C1-18alkyl; Y− is an anion. The mentioned compounds can be applied to staining biological samples, to the fields of nucleic acids labeling, blood cell analysis, clinical diagnosis, immunological assays and etc.