The suspects, in their mid-30s, were arrested during a joint investigation with the FBI and Israel's cyber crime unit. Further arrests were made in France, Germany, the Netherlands and Brazil.
"The suspects were arrested after setting up an Internet site that was in the 'dark'," the police said in a statement. "The dark internet site was used for illegal activities and crimes.
"The site had been active for a long period of time and millions of dollars of transactions had been made on the site."
The police said the site guided users to other sites used for illegal activities and crimes which were being investigated.
"The sites worked together covering each other and marketing illegal actions and transactions," police said, adding that the transactions were made using Bitcoin.
The two Israeli suspects are due to appear before a Tel Aviv court. No further details were given.
Three German nationals accused of running one of the world's largest dark websites for selling drugs and other contraband were arrested last week and charged in two countries following a two-year investigation.
A fourth man who allegedly acted as a moderator and promoter for the site was taken into custody in Brazil.