At first they called their station Hymann-Almy-Murray. Tapping it out in code called for a revision and they changed it to HY-AL-MU, using the first two letters of each name.

Early in 1909, some confusion resulted between signals from amateurs wireless HYALMU and a Mexican ship named 'Hyalmo', so they decided to use only the first letter of each name and the call became 'HAM'.

In the early pioneer unregulated days of radio, amateurs picked their own frequency and call letters. Some had, as now, better signals than some commercial stations. The resulting interference came to the attention of Congressional committees in Washington and they gave much time to proposed legislation designed to critically limit amateur activity.
In 1911, Albert Hymann chose the controversial wireless regulation bill as the topic for his thesis at Harvard. A copy was send to senator David Walsh. The senator was so impressed, he sent for Hymann to appear before the committee. He was put on the stand and described how the little amateur station was built and he almost cried when he told the crowded committee room that if the bill went through, they would have to close up the station because they could not afford the licence fees and all the other requirements which were set up in the bill. The debate started and the little station "HAM" became a symbol of all the little amateur stations in the country crying out to be saved from menace and greed of the big commercial stations who didn't want them around.
Finally, the bill got to the floor of Congress and every speaker talked about the poor little station 'HAM'.

That's how it all started. You will find the whole story in the Congressional record. Nationwide publicity associated station "HAM" with amateurs. From that day to this and probably to the end of time, in radio, an Amateur is a 'HAM'.