Yes, but you have to be careful. By default, colormap() applies to the current figure. If you want it to apply to the current axes alone, you can specify the axes object.
RGB = imread('flowers.png');
[X,cmap] = rgb2ind(RGB,32);
RGB2 = imread('shoes.png');
[X2,cmap2] = rgb2ind(RGB2,32);
A = reshape(1:36, 6, 6); % A = reshape(1:256, 16, 16);
subplot(2,2,1)
imshow(RGB)
title('Original RGB Image')
subplot(2,2,2);
imshow(RGB2);
title('Target Image')
colormap(cmap2);
colorbar;
hax = subplot(2,2,3);
image(A);
colormap(hax,cmap);
colorbar;
title('Colormap A')
hax = subplot(2,2,4);
image(A);
colormap(hax,cmap2);
colorbar;
title('Colormap B')
Two things to note: First, I reordered the subplots so that it would be readable on the forum. Second, since the swatch charts are basically indexed color images, we should be using image() instead of imagesc() so that the colormapping is direct. Alternatively, if using imshow(), you would use something like
imshow(A,cmap)
colorbar;
instead of calling colormap() explicitly.