Different fluorochromes might need different excitation wavelengths. But fluorochromes that can be excitated with the same wavelength can have different emission wavelengths. This makes it possible to measure signals from different fluorochromes in a flow cytometer with one laser (= one wavelength).
A fluorescence microscope uses a high powered mercury lamp. This lamp has a large part of the spectrum and is able to excitate more different fluorochromes. Both flow cytometer and microscope use filters to select for the specific emission. Excitation and emission wavelength determine the fluorochrome(s) that can be used.

Figure.1.A. Normalized fluorescence emission spectra of goat anti–mouse IgG conjugates of 1) fluorescein, 2) rhodamine 6G, 3) tetramethylrhodamine, 4) Lissamine rhodamine B and 5) Texas Red dyes. (figure taken from the Handbook of fluorescent Probes and Research Chemicals from Molecular Probes (fig.1.10))

Probe	Ex (nm)	Em (nm)	Alternative name
Cascade Blue	375;400	423
Lucifer yellow	425	528
NBD	466	539
R-Phycoerythrin (PE)	480;565	578
PE-Cy5 conjugates	480;565;650	670	Tri-Color, Quantum Red
PE-Cy7 conjugates	480;565;743	767
Red 613	480;565	613	PE-Texas Red
PerCP	490	675	Peridinin chlorphyll protein
TrueRed	490,675	695	PerCP-Cy5.5 conjugate
Fluorescein	495	519	FITC
BODIPY-FL	503	512
Cy3	512;552	565,615
TRITC	547	572	TRITC
X-Rhodamine	570	576	XRITC
Lissamine Rhodamine B	570	590
Texas Red	589	615	Sulfonyl chloride
Cy5	625-650	670
Allophycocyanin (APC)	650	660
APC-Cy7 conjugates	650;755	767	PharRed
Cy7	743	767

Table.1.B. Excitation (ex) and emission (em) of generally used fluorochromes in order of their ex wavelength.