The men, aged 32 and 31, were arrested early this morning, Wednesday 6th February.
They will be questioned throughout the day.
The arrests come as searches at Maize Farm, in East Heckington, Lincolnshire, continue.
Detectives have been joined by a number of experts and specialists who can offer advice and information about the site.
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James Brodie, who was 19, is believed to have gone missing shortly after jeweller Ravenshead Marian Bates was shot dead during a robbery at the Time Centre, in Arnold, in September 2003.
He has not made any contact with family or friends in more than nine years.