|MadSci Network: Science History|
Based on information from Wikipedia, it appears that Mendel's publication of his work in 1866 received very little attention. It was not until 1900, about 16 years after his death, when his work was rediscovered and widely acknowledged (1). Apparently, the concept of genetic linkage was co-discovered by William Bateson and Reginald Punnett some time after the rediscovery of Mendel's work (2), so Mendel would not have known about linkage at the time of his studies.
This brings up an interesting question of why Mendel did not observe any examples of co-inheritance of traits when he crossed his pea plants. One possibility is that he happened to focus on traits which, in peas, are not genetically linked. But it has also been suggested that Mendel may have "discarded" or failed to report observations which did not fit well with his hypotheses (1).
If you're interested in reading more about Mendel, you might try "The Monk in the Garden" by Robin Henig. It seems to have received mixed reviews on Amazon.com (3), and I have not personally read it, but it may have more information.
(3) http://www.amazon.com/-Monk-Garden-Lost-Found-Genius-Gregor-Mendel- Father-Genetics/dp/0618127410/sr=1-1/qid=1158779753/ref=pd_bbs_1/104-0351944-0101568? ie=UTF8&s=books
Try the links in the MadSci Library for more information on Science History.