Step 1: Recall RAPD.
RAPD (Random Amplified Polymorphic DNA) is a PCR-based technique that uses short arbitrary primers to amplify random DNA segments.
Step 2: Identify its limitation.
Because RAPD is highly sensitive to PCR conditions such as DNA quality, primer concentration and annealing temperature, its results are often difficult to reproduce.
Thus,
\[
\boxed{\text{Poor reproducibility}}
\]
is the major limitation of RAPD.
Therefore,
\[
\boxed{(B)}
\]
is the correct answer.