Four full-sib families of Oncorhynchus mykiss were used to study the inheri
tance of allelic variation at 12 microsatellite loci. The loci examined wer
e previously characterized in six different species from the family Salmoni
dae, Of the 48 genotypic ratios observed (12 loci x 4 crosses), disomic seg
regation of codominant autosomal alleles was established in 24 of 31 inform
ative tests, The seven tests that did not conform to Mendelian ratios can b
e explained by the presence of null alleles (One mu 14 and Omy77) and a loc
us (One mu 1) that may be tandemly duplicated. Three significant pairwise l
inkage associations were observed between One mu 1 and Omy207, Ssa85 and On
e mu 11, and the two loci amplified by One mu 1 primers, indicating these l
oci are not asserting independently. The presence of unexpected heteroduple
x structures in One mu 11 electropherograms in one cross prompted the seque
ncing of similar microsatellite electromorphs. Sequence differences reveale
d size homoplasy, that is, the electromorphs were identical in state but th
ey were not identical by descent. These results demonstrate the need to con
duct comprehensive species-specific inheritance studies for microsatellite
loci used in population genetic or kinship analyses. Discovery of these fou
r attributes by examining a small number of loci in four families suggests
that they are common across microsatellite loci overall.