Anelka lashed the ball home from inside the area to give the Wanderers their first Premiership win of the year and in turn end a winless streak which had stretched back nearly a month.
Neither goalkeeper had much to do in a quiet afternoon in Hertfordshire but Bolton will be releived that they have been able to put some distance between themselves and the other clubs who are also in the chase for a UEFA Cup spot.
Prior to kick off Bolton had doubts about the fitness of defender Abdoulaye Faye and Anelka but it's just as well that the former Manchester City striker was passed fit to score his first goal in seven matches.
Anelka warned Watford of the dangers to come as early as the third minute when he fired in a powerfully accurate free kick from all of 30-yards which just dipped over the crossbar of goalkeeper Ben Foster.
Watford could have put their noses in front at the other end on 22 minutes when a free kick from Hameur Bouazza was headed over by American defender Jay DeMerit.
Former Leicester City player Jordan Stewart was next to fire in an attempt on goal for the Hornets but his shot from distance failed to test the Bolton keeper Jussi Jaaskelainen who had a relatively easy afternoon.
Watford skipper Gavin Mahon also tried his luck from afar with his effort going well wide of the mark but Bolton had better luck five minutes before the break when Anelka's rasping drive forced a save out of Foster.
Wanderers forward El-Hadji Diouf made inrodes down the left flank to cross for Gary Speed as the half ticked to a close. The Welshman diverted his header towards goal but their wasn't enough power or accuracy behind the effort to break the deadlock.
After the interval the game was desperate for a goal and Bolton introduced Iran midfielder Andranik Teimourian in place of the out of sorts Stelios Giannakopoulos. Teimourian immediately made an impact by forcing Foster to get down low and make a 57th minute save.
Bolton's pressure finally told on 63 minutes when goalkeeper Foster only parried a corner by Speed into the path of the waiting Anelka who duly fired the ball home from close proximaty.
The home side went desperately in search of an equaliser as they introduced recent signings Steve Kabba and Gareth Williams from the substitutes bench but Bolton defended firmly to cling onto their one goal advantage.
In the final minute veteran defender Malky Mackay found himself through on goal but Bolton keeper Jaaskelainen came out to avert the danger. Many of the home support thought the Finn had handled the ball outside the area and wanted to see a dismissal but referee Rob Styles used common sense in just booking the Scandanavian stopper.
Bolton Wanderers: Jussi Jaaskelainen, Nicky Hunt, Abdoulaye Faye, Abdoulaye Meite, Tal Ben-Haim, Kevin Nolan, Ivan Campo, Gary Speed, Stelios Giannakopoulos (Andranik Teimourian), Nicolas Anelka, El-Hadji Diouf (Henrik Pedersen)
Subs Not Used: Ricardo Gardner, Idan Tal, Ian Walker (GK)
Watford: Ben Foster, Adrian Mariappa, Malky Mackay, Jay DeMerit, Jordan Stewart, Lee Williamson (Gareth Williams), Gavin Mahon, Damien Francis (Steve Kabba), Hameur Bouazza (Anthony McNamee), Darius Henderson, Will Hoskins
Subs Not Used: Lloyd Doyley, Richard Lee (GK)
Referee:
Rob Styles
Attendance:
18,722
Booked:
Abdoulaye Faye (Bolton)
Andranik Teimourian (Bolton)
Jussi Jaaskelainen (Bolton)
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