R help - May 2011 - permutation/randomization test assumption on observations

Hi,

I have two groups of data of different size:
? ?group A: x1, x2, ...., x_n;
? ?group B: y1, y2, ...., y_m; (m is not equal to n)

The two groups are independent but observations within each group are
not independent,
  i.e., x1, x2, ..., x_n are not independent; but x's are independent from
y's

I wonder if randomization test is still applicable to this case; if
so, anything I have to pay attention?

Thank you very much,
Wenjin