If genes are linked then they act as if they are on the same chromosome. That is to say whenever gene A is observed so is gene B. However, for non-sex chromosomes, each person has 2 of the "same" autosome, one from the maternal line and the other from the paternal line. There is a chance that recombination will take place between these the paternal and maternal autosome thereby making a hybrid paternal and maternal chromsome. If the genes are physically far apart on the chromsome there is a higher frequency that they will undergo recombination (the shuffling stuff that makes the hybrid chromosome.) If the genes are physically really close, then there is a lower frequency of recombination.
By physically I mean literally mean physically, i.e. number of base pairs apart.