In addition to mercenaries, the local militia system was in force on Candia. This was composed of different local classes - peasants, citizens, and feudal vassals - each organised into its own militia or company. The institution of the citizen militia dated back to the early sixteenth century, while the organisation of the peasant militia originated in the 1570s. Between the sixteenth century and the early seventeenth century the number of those in the militia numbered around 12,000 men. Two-thirds of these came from campaigns, while the remaining third were placed in companies in Candia , Rethymno , Chania  and Siteia . The difference in arms carried by the citizen and the rural militia reveals the profound division separating these two worlds: the city troops (or 'cernide'  as they were called) were equipped with firearms such as arquebuses and muskets, while about 10-20% of the men carried pikes . Instead, the rural militia were armed only with bows, and firearms did not make their appearance here until the mid-seventeenth century.

In exchange for tax exemptions, the 'cernide' were obliged to drill with arms at certain times of the year under the supervision of Italian and Greek officials.