Use groupsummary.
C1 = [1 1 1 1 1 2 2 2 2 2 2 3 3 3 4 4 4 4].';
C2 = [5 10 12 35 3 1 4 26 5 11 12 8 2 22 8 2 5 7].';
[binvalues, bingroups] = groupsummary(C2, C1, @sum)
This applies the sum function to each group of elements in C2 for which the corresponding values in C1 are the same. Each element of binvalues is the sum of the elements in C2 for the bin in the corresponding element of bingroups.
The elements of C1 don't need to be positive integers; I could have grouped the values corresponding to bins associated with C1+1.5 if I wanted.
